Comparative Genomics Reveals a Remarkable Biosynthetic Potential of the
            <i>Streptomyces</i>
            Phylogenetic Lineage Associated with Rugose-Ornamented Spores

Chung, Yoon-Hee; Kim, Hiyoung; Ji, Chang-Hun; Je, Hyun-Woo; Lee, Dong‐Ho; Shim, Sang Hee; Joo, Hwang-Soo; Kang, Hahk‐Soo

doi:10.1128/msystems.00489-21

Cited by 15 publications

(11 citation statements)

References 48 publications

(53 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In previously reported Streptomyces CRISPR/Cas9 systems, the two most commonly used promoters for Cas9 expression have been rpsL p and ermE* p. , To evaluate species-specific variations, we compared the transcriptional strengths of these two promoters in four phylogenetically diverse Streptomyces species using the IndC gene as a reporter (Figure B). The strains Streptomyces albidoflavus J1074 (SA), Streptomyces roseosporus NRRL11379 (SR), and Streptomyces coelicolor A3(2) (SC) were included because they are widely used, well-known Streptomyces strains that are also phylogenetically distinct from each other. − The strain Streptomyces yatensis DSM41771 (SY) was also included as a model strain of a phylogenetic lineage characterized by the largest genome (>11 Mb) containing the largest number of BGCs (on average 50 BGCs per genome), many of which are silent under normal laboratory culture conditions. , As measured by the amount of indigoidine production, the rpsL promoter displayed a higher promoter strength than ermE* in S. albidoflavus and S.…”

Section: Resultsmentioning

confidence: 99%

CaExTun: Mitigating Cas9-Related Toxicity in Streptomyces through Species-Specific Expression Tuning with Randomized Constitutive Promoters

Kim

et al. 2022

ACS Synth. Biol.

Self Cite

View full text Add to dashboard Cite

The CRISPR/Cas9 system provides an efficient tool for engineering genomes. However, its application to Streptomyces genome engineering has been hampered by excessive toxicity associated with overexpression of Cas9 protein. As the level of Cas9 toxicity varies significantly between Streptomyces species, species-specific optimization of Cas9 expression is a strategy to mitigate its toxicity while maintaining sufficient double-strand break (DSB) activity for genome engineering. Using a pool of randomized constitutive promoters and a blue pigment indigoidine biosynthetic gene (IndC) as a reporter, we developed the CaExTun (Cas9 Expression Tuning) platform, which enables rapid screening of a large pool of promoter–Cas9 constructs to quickly recover the one with high DSB activity and no apparent toxicity. We demonstrate the utility of CaExTun using four model Streptomyces species. We also show that CaExTun can be applied to the CRISPRi system by allowing the construction of a library of promoter–dCas9 constructs that confer a wide range of gene repression levels. As demonstrated here, CaExTun is a versatile tool for the rapid optimization of the CRISPR/Cas9 system in a species-specific manner and thus will facilitate CRISPR/Cas9-based genome engineering efforts in Streptomyces.

show abstract

Section: Resultsmentioning

confidence: 99%

CaExTun: Mitigating Cas9-Related Toxicity in Streptomyces through Species-Specific Expression Tuning with Randomized Constitutive Promoters

Kim

et al. 2022

ACS Synth. Biol.

Self Cite

View full text Add to dashboard Cite

show abstract

“…We found that AgN23 genome, as well as other representative strains of the S. violaceusniger clade is rich in CAZymes able to degrade plant-derived carbohydrates and in BGCs producing specialised metabolite potentially involved in the interaction with the plant. In addition, this phylogenetic lineage is considered as having a high potential in terms of specialised metabolism as its members have a large genome between 10.7 and 12.7 Mb and possess from 45 to 55 BGCs [90]. The wealth of genomic data available in this clade allowed us to unveil common trends in the BGCs specifically found in S. violaceusniger isolates.…”

Section: Discussionmentioning

confidence: 99%

Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

Gayrard

Veyssière

Adam

et al. 2021

Preprint

View full text Add to dashboard Cite

Streptomycetes are Gram-positive actinobacteria largely represented in the plant root microbiota. The genetic determinants involved in the presence of Streptomyces in the rhizosphere are largely unknown and can rely on the ability to degrade plant-derived compounds such as cell-wall polysaccharides and on the production of specialised metabolites. To address whether Streptomyces strains recruited into root microbiota share genomic specificities related to these two functions, we engaged a comparative genomic analysis using a newly sequenced rhizospheric strain, Streptomyces sp. AgN23 and strains from the phylogenetically related S. violaceusniger clade. This analysis enlightens a shared prominent CAZyome potentially involved in plant polysaccharides degradation and a strong conservation of antimicrobials biosynthetic clusters (rustmicin, mediomycin, niphimycin, nigericin) as well as plant bioactive compounds (nigericin, echosides, elaiophylin). Taken together, our work supports the hypothesis that specific hydrolytic enzymes and specialised metabolites repertoires may play important roles in the development of Streptomyces strains in the rhizosphere.

show abstract

“…These Streptomyces strains were also described as a specific phylogenetic lineage with the highest BGC abundance and largest genome size across diverse Streptomyces-type strains. 48 There is currently some evidence suggests potential complex cross-BGC regulation in this class of Streptomyces strains: Jiang et al demonstrated that a TetR family transcriptional regulator, GdmRIII, controls the biosynthesis of geldanamycin and elaiophylin meanwhile, in Streptomyces autolyticus CGMCC 0516. 49 Recently, He et al found that the rapamycin BGC-situated LAL family regulator RapH co-ordinately regulated the biosynthesis of both rapamycin and elaiophylin in S. rapamycinicus NRRL 5491.…”

Section: Phylogenetic and Evolutionary Analysis Of Pta Bgcmentioning

confidence: 99%

Streptomyces alleviate abiotic stress in plant by producing pteridic acids

Yang

Strøbech

Qiao

et al. 2022

Preprint

View full text Add to dashboard Cite

Soil microbiota can confer fitness advantages to plants and increase crop resilience to drought and other abiotic stressors. However, there is little evidence on the mechanisms correlating a microbial trait with plant abiotic stress tolerance. Here, we report that a class of Streptomyces effectively alleviates the drought and salinity stress by producing new spiroketal polyketide pteridic acid H (1) and its isomer F (2). The bifunctional pteridic acid (pta) biosynthetic gene cluster (BGC), which is also responsible for the biosynthesis of the known antimicrobial elaiophylin, was confirmed by bioinformatic analysis and in vivo CRISPR base editing. Pteridic acids H and F exhibited profound effects in promoting root growth in Arabidopsis at a concentration of 0.5 ng mL-1 (1.3 nM) under abiotic stress, indicating they are a new class of plant stress regulators. Phylogenetic and geographical distribution analysis revealed that the pta BGC was mainly disseminated by vertical transmission and occasional horizontal gene transfer and is widely distributed in numerous Streptomyces in different environments. This discovery reveals a new perspective for understanding plant-Streptomyces interactions and provides a novel, promising approach for utilising beneficial Streptomyces and their secondary metabolites in agriculture to mitigate the detrimental effects of climate change.

show abstract

Comparative Genomics Reveals a Remarkable Biosynthetic Potential of the Streptomyces Phylogenetic Lineage Associated with Rugose-Ornamented Spores

Cited by 15 publications

References 48 publications

CaExTun: Mitigating Cas9-Related Toxicity in Streptomyces through Species-Specific Expression Tuning with Randomized Constitutive Promoters

CaExTun: Mitigating Cas9-Related Toxicity in Streptomyces through Species-Specific Expression Tuning with Randomized Constitutive Promoters

Genomic adaptation in the CAZyome and specialised metabolism of the plant-associated Streptomyces violaceusniger clade

Streptomyces alleviate abiotic stress in plant by producing pteridic acids

Contact Info

Product

Resources

About