The genome sequence of Streptomyces rochei 7434AN4, which carries a linear chromosome and three characteristic linear plasmids

Nindita, Yosi; Cao, Zhisheng; Fauzi, Amirudin Akhmad; Teshima, Aiko; Misaki, Y.; Muslimin, Rukman; Yang, Yingjie; Shiwa, Yuh; Yoshikawa, Hideki; Tagami, Michihira; Lezhava, Alexander; Ishikawa, Jun; Kuroda, Makoto; Sekizuka, Tsuyoshi; Inada, Kazuo; Kinashi, Haruyasu; Arakawa, Kenji

doi:10.1038/s41598-019-47406-y

Cited by 30 publications

(30 citation statements)

References 52 publications

(76 reference statements)

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“…All data were obtained from previous studies [1,15,26,32]. T1pks-6 or t1pks-7 is the predicted ctr cluster for citreodiol and epi-citreodiol [33].…”

Section: Emended Description Of Streptomyces Murinus Frommer 1959 (Apmentioning

confidence: 99%

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Reclassification of Streptomyces costaricanus and Streptomyces phaeogriseichromatogenes as later heterotypic synonyms of Streptomyces murinus

Komaki

2021

International Journal of Systematic and Evolutionary Microbiology

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This study aimed to clarify the taxonomic relationships among Streptomyces costaricanus , Streptomyces graminearus, Streptomyces murinus and Streptomyces phaeogriseichromatogenes . These strains share the same 16S rRNA gene sequence. Multilocus sequence analysis revealed that S. costaricanus , S. murinus and S. phaeogriseichromatogenes belong to the same species, but S. graminearus does not. Digital DNA–DNA relatedness and average nucleotide identity among S. costaricanus, S. murinus and S. phaeogriseichromatogenes were 70.9–74.6% and 96.5–97.0 %, respectively. In addition to the previously reported phenotypic data, the presence of a similar set of secondary metabolite-biosynthetic gene clusters for polyketides and nonribosomal peptides supported the similarity among the three species. Therefore, S. costaricanus and S. phaeogriseichromatogenes should be reclassified as later heterotypic synonyms of S. murinus .

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“…All data were obtained from previous studies [1,15,26,32]. T1pks-6 or t1pks-7 is the predicted ctr cluster for citreodiol and epi-citreodiol [33].…”

Section: Emended Description Of Streptomyces Murinus Frommer 1959 (Apmentioning

confidence: 99%

“…murinus NRRL B-2286 T . T1pks-6 or t1pks-7 is the predicted ctr cluster for citreodiol and epi -citreodiol [33].…”

Section: Full-textmentioning

confidence: 99%

Reclassification of Streptomyces costaricanus and Streptomyces phaeogriseichromatogenes as later heterotypic synonyms of Streptomyces murinus

Komaki

2021

International Journal of Systematic and Evolutionary Microbiology

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“…In the genome mining study, we have identified several known BGC, studied in other strains. Among these are lankacidin and lankamycin BGCs, encoded on plasmid pSGRIFU1, previously studied in S. rochei (40, 41) and pentamycin BGC33 (42). Due to the good preservation of these BGCs in the genome we expected to detect the production of lankamycin, lankacidin-family compounds and pentamycin.…”

Section: Resultsmentioning

confidence: 99%

Characterization and Engineering ofStreptomyces griseofuscusDSM 40191 as a Potential Host for Heterologous Expression of Biosynthetic Gene Clusters

Gren

Whitford

Mohite

et al. 2020

Preprint

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Streptomyces griseofuscus DSM 40191 is a fast growing Streptomyces strain that remains largely underexplored as a heterologous host. Here, we report the genome mining of S. griseofuscus, followed by the detailed exploration of its phenotype, including production of native secondary metabolites and ability to utilise carbon, nitrogen, sulphur and phosphorus sources. Furthermore, several routes for genetic engineering of S. griseofuscus were explored, including use of GusA-based vectors, CRISPR-Cas9 and CRISPR-cBEST-mediated knockouts. Using CRISPR-BEST technology, core genes of 4 biosynthetic gene clusters (BGCs) that are situated on the chromosome arms were inactivated and the outcomes of the inactivations were tested. Two out of the three native plasmids were cured using CRISPR-Cas9 technology, leading to the generation of strain S. griseofuscus DEL1. DEL1 was further modified by full deletion of a pentamycin BGC and an unknown NRPS BGC, leading to the generation of strain DEL2, lacking approx. 500 kbp of the genome, which corresponds to a 5,19% genome reduction. Sequencing confirmed that DEL2 does not bear any crucial off-target effects or rearrangements in its genome. It can be characterized by faster growth and inability to produce three main native metabolites of S. griseofuscus: lankacidin, lankamycin, pentamycin and their derivatives. To test the ability of DEL2 to heterologously produce secondary metabolites, the actinorhodin BGC was used. We were able to confirm the production of actinorhodin by both S. griseofuscus wild type and DEL2. We believe that this strain will serve as a good chassis for heterologous expression of BGCs.ImportanceThe rise of antibacterial resistance calls on the development of the next generation of antibiotics, majority of which are derived from natural compounds, produced by actinomycetes. The manipulation, refactoring and expression of BGCs coding for such natural products is a promising approach in secondary metabolite discovery. Thus, the development of a versatile panel of heterologous hosts for the expression of BGCs is essential. We believe that first-to-date systematic, detailed characterisation of S. griseofuscus, a highly promising chassis strain, will not only facilitate the further development of this particular strain, but also will set a blueprint for characterisation of other potential hosts.

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“…To our surprise, azoxyalkene compound KA57-A accumulated in a triple knockout mutant of S. rochei that have mutations on two biosynthetic gene clusters for LC, LM, and srrB (Kunitake et al, 2015). The genome sequence of the S. rochei chromosome has been determined to be 8.36 Mb in size, and at least 35 secondary metabolites gene clusters are coded on the chromosome (Nindita et al, 2019). Comprehensive mutational analysis on various regulatory genes may lead to activate silent secondary metabolite gene clusters in S. rochei, which is in progress in our laboratory.…”

Section: Discussionmentioning

confidence: 96%

SrrB, a Pseudo-Receptor Protein, Acts as a Negative Regulator for Lankacidin and Lankamycin Production in Streptomyces rochei

et al. 2020

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Streptomyces rochei 7434AN4, a producer of lankacidin (LC) and lankamycin (LM), carries many regulatory genes including a biosynthesis gene for signaling molecules SRBs (srrX), an SRB receptor gene (srrA), and a SARP (Streptomyces antibiotic regulatory protein) family activator gene (srrY). Our previous study revealed that the main regulatory cascade goes from srrX through srrA to srrY, leading to LC production, whereas srrY further regulates a second SARP gene srrZ to synthesize LM. In this study we extensively investigated the function of srrB, a pseudo-receptor gene, by analyzing antibiotic production and transcription. Metabolite analysis showed that the srrB mutation increased both LC and LM production over four-folds. Transcription, gel shift, and DNase I footprinting experiments revealed that srrB and srrY are expressed under the SRB/SrrA regulatory system, and at the later stage, SrrB represses srrY expression by binding to the promoter region of srrY. These findings confirmed that SrrB acts as a negative regulator of the activator gene srrY to control LC and LM production at the later stage of fermentation in S. rochei.

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The genome sequence of Streptomyces rochei 7434AN4, which carries a linear chromosome and three characteristic linear plasmids

Cited by 30 publications

References 52 publications

Reclassification of Streptomyces costaricanus and Streptomyces phaeogriseichromatogenes as later heterotypic synonyms of Streptomyces murinus

Reclassification of Streptomyces costaricanus and Streptomyces phaeogriseichromatogenes as later heterotypic synonyms of Streptomyces murinus

Characterization and Engineering ofStreptomyces griseofuscusDSM 40191 as a Potential Host for Heterologous Expression of Biosynthetic Gene Clusters

SrrB, a Pseudo-Receptor Protein, Acts as a Negative Regulator for Lankacidin and Lankamycin Production in Streptomyces rochei

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