Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery

Alberti, Fabrizio; Leng, Daniel J.; Wilkening, Ina; Song, Lijiang; Tosin, Manuela; Corre, Christophe

doi:10.1039/c8sc03814g

Cited by 43 publications

(35 citation statements)

References 35 publications

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“…[29][30][31] It is interesting, however, that pCRISPomyces-2 has not yet been reported to work in S. coelicolor, which is considered the model species among streptomycetes. At the time of writing, there is only one published report of attempting its use in S. coelicolor, which was described as unsuccessful, 17 similarly to what reported for the same plasmid in Streptomyces sp. KY 40-1.…”

Section: Critical Analysis Of Current Toolkits and Prospectsmentioning

confidence: 78%

“…16 For instance, using a combination of TAR cloning to capture a cryptic and silent BGC and pCRISPomyces-2 (Section 3.2) to inactivate one of the cluster-specic transcriptional repressors, our group have recently discovered and characterised the biosynthesis of the novel L-proline derivative scleric acid (4). 17 Other potential and critical issues, more specic to CRISPR/ Cas9 systems are: (i) toxicity of Cas9 in the specic strain used, as reported by Rohr and colleagues in Streptomyces sp. KY 40-1 (ref.…”

Section: Key Considerationsmentioning

confidence: 99%

“…10 Since its release, pCRISPomyces-2 has been successfully employed by other groups to edit the genome of various streptomycetes, demonstrating its potential for the engineering of both established hosts and other less commonly used strains. 17,[24][25][26][27][28][29][30][31] For instance, Hutchings and collaborators used it to generate both one-gene and whole-cluster deletions in Streptomyces formicae to conrm the identity of the antibiotic formicamycin (5) BGC and study the activity of the clusterincluded halogenase ForV. 25 The plasmid pCRISPomyces-2 was also employed by Zhang and colleagues to generate pointmutations and small deletions to increase oxytetracycline (6) production in Streptomyces rimosus, 26 as well as by Metsä-Ketela and colleagues to investigate glycosylation of the nucleoside antibiotic showdomycin (7) in Streptomyces showdoensis.…”

Section: Pcrispomyces Plasmids From Zhao and Colleagues 10mentioning

confidence: 99%

“…Among these toolkits, pCRISPomyces-2 (ref. 10) is the plasmid that has seen the highest number of applications, 17,[24][25][26][27][28][29][30][31] showing also the potential to be used in non-streptomycete Grampositive and even Gram-negative bacteria. [29][30][31] It is interesting, however, that pCRISPomyces-2 has not yet been reported to work in S. coelicolor, which is considered the model species among streptomycetes.…”

Section: Critical Analysis Of Current Toolkits and Prospectsmentioning

confidence: 99%

See 3 more Smart Citations

Editing streptomycete genomes in the CRISPR/Cas9 age

Alberti

Corre

2019

Nat. Prod. Rep.

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Section: Critical Analysis Of Current Toolkits and Prospectsmentioning

confidence: 78%

Section: Key Considerationsmentioning

confidence: 99%

Section: Pcrispomyces Plasmids From Zhao and Colleagues 10mentioning

confidence: 99%

Section: Critical Analysis Of Current Toolkits and Prospectsmentioning

confidence: 99%

See 2 more Smart Citations

Editing streptomycete genomes in the CRISPR/Cas9 age

Alberti

Corre

2019

Nat. Prod. Rep.

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“…nutrient deprivation [21]. Additionally, the activation of dormant BGCs through genetic manipulation resulting in the production of a new antimicrobial compound has recently been reported [23]. The results from co-cultures with pre-cultured S-2 suggest a constitutive production of antifungal agents by the strain.…”

Section: Discussionmentioning

confidence: 97%

Genome Mining Revealed a High Biosynthetic Potential for Antifungal Streptomyces sp. S-2 Isolated from Black Soot

Siupka

Piński

Babicka

et al. 2020

IJMS

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The increasing resistance of fungal pathogens has heightened the necessity of searching for new organisms and compounds to combat their spread. Streptomyces are bacteria that are well-known for the production of many antibiotics. To find novel antibiotic agents, researchers have turned to previously neglected and extreme environments. Here, we isolated a new strain, Streptomyces sp. S-2, for the first time, from black soot after hard coal combustion (collected from an in-use household chimney). We examined its antifungal properties against plant pathogens and against fungi that potentially pose threat to human health (Fusarium avenaceum, Aspergillus niger and the environmental isolates Trichoderma citrinoviridae Cin-9, Nigrospora oryzae sp. roseF7, and Curvularia coatesieae sp. junF9). Furthermore, we obtained the genome sequence of S-2 and examined its potential for secondary metabolites production using anti-SMASH software. The S-2 strain shows activity against all of the tested fungi. Genome mining elucidated a vast number of biosynthetic gene clusters (55), which distinguish this strain from closely related strains. The majority of the predicted clusters were assigned to non-ribosomal peptide synthetases or type 1 polyketide synthetases, groups known to produce compounds with antimicrobial activity. A high number of the gene clusters showed no, or low similarity to those in the database, raising the possibility that S-2 could be a producer of novel antibiotics. Future studies on Streptomyces sp. S-2 will elucidate its full biotechnological potential.

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Characterization of Cas proteins for CRISPR‐Cas editing in streptomycetes

Yeo

Heng

Tan

et al. 2019

Biotech & Bioengineering

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Application of the well-characterized Streptococcus pyogenes CRISPR-Cas9 system in actinomycetes streptomycetes has enabled high-efficiency multiplex genome editing and CRISPRi-mediated transcriptional regulation in these prolific bioactive metabolite producers. Nonetheless, SpCas9 has its limitations and can be ineffective depending on the strains and target sites. Here, we built and tested alternative CRISPR-Cas constructs based on the standalone pCRISPomyces-2 editing plasmid.We showed that Streptococcus thermophilus CRISPR1 Cas9 (sth1Cas9), Staphylococcus aureus Cas9 (saCas9), and Francisella tularensis subsp. novicida U112 Cpf1 (fnCpf1) are functional in multiple streptomycetes, enabling efficient homology-directed repairmediated knock-in and deletion. In strains where spCas9 was nonfunctional, these alternative Cas systems enabled precise genomic modifications within biosynthetic gene clusters for the discovery, production, and diversification of natural products.These additional Cas proteins provide us with the versatility to overcome the limitations of individual CRISPR-Cas systems for genome editing and transcriptional regulation of these industrially important bacteria.

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Triggering the expression of a silent gene cluster from genetically intractable bacteria results in scleric acid discovery

Abstract: The characterisation of scleric acid, a new natural product from a silent and cryptic gene cluster from genetically intractable bacteria, and its biosynthesis are reported.

Cited by 43 publications

References 35 publications

Editing streptomycete genomes in the CRISPR/Cas9 age

Editing streptomycete genomes in the CRISPR/Cas9 age

Genome Mining Revealed a High Biosynthetic Potential for Antifungal Streptomyces sp. S-2 Isolated from Black Soot

Characterization of Cas proteins for CRISPR‐Cas editing in streptomycetes

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