sRNA scr5239 Involved in Feedback Loop Regulation of Streptomyces coelicolor Central Metabolism

Engel, Franziska; Ossipova, Elena; Jakobsson, Per‐Johan; Vockenhuber, Michael-Paul; Suess, Beatrix

doi:10.3389/fmicb.2019.03121

Cited by 8 publications

(5 citation statements)

References 42 publications

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“…Thus, RpoE, RpoHII, and StsR form a negative feed-back loop consisting of protein regulators and sRNA. Such regulatory loops have been reported for other bacteria (e.g., [ 51 , 52 , 53 , 54 ]). Regulation in the RpoE-RpoHII-StsR loop is based on different mechanisms.…”

Section: Discussionsupporting

confidence: 74%

A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides

Eisenhardt

Remes

Grützner

et al. 2021

IJMS

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Adaptation of bacteria to a changing environment is often accompanied by remodeling of the transcriptome. In the facultative phototroph Rhodobacter sphaeroides the alternative sigma factors RpoE, RpoHI and RpoHII play an important role in a variety of stress responses, including heat, oxidative stress and nutrient limitation. Photooxidative stress caused by the simultaneous presence of chlorophylls, light and oxygen is a special challenge for phototrophic organisms. Like alternative sigma factors, several non-coding sRNAs have important roles in the defense against photooxidative stress. RNAseq-based transcriptome data pointed to an influence of the stationary phase-induced StsR sRNA on levels of mRNAs and sRNAs with a role in the photooxidative stress response. Furthermore, StsR also affects expression of photosynthesis genes and of genes for regulators of photosynthesis genes. In vivo and in vitro interaction studies revealed that StsR, that is under control of the RpoHI and RpoHII sigma factors, targets rpoE mRNA and affects its abundance by altering its stability. RpoE regulates expression of the rpoHII gene and, consequently, expression of stsR. These data provide new insights into a complex regulatory network of protein regulators and sRNAs involved in defense against photooxidative stress and the regulation of photosynthesis genes.

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Section: Discussionsupporting

confidence: 74%

A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides

Eisenhardt

Remes

Grützner

et al. 2021

IJMS

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“…Some software use this information to predict novel sRNAs in bacterial genomes such as RNAz ( Gruber et al, 2010 ) and QRNA ( Sridhar and Gunasekaran, 2013 ). Since little is known about the abundance and function of sRNA in Gram-positive bacteria like Streptomyces ( Engel et al, 2020 ), an accurate determination of the conservation of IGRs and its dependency with phylogenetic distance is necessary for a proper estimation of regulatory RNAs encoding potential ( Tsai et al, 2015 ). The current analysis shows that IGRs conservation is reduced at the level of genus and the conservation is still low in smaller groups, when strains are grouped according to the three clades obtained in the phylogenetic tree.…”

Section: Discussionmentioning

confidence: 99%

Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds

2021

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Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.

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“…Among 2160 Gram-positive bacteria (Firmicutes and Actinobacteria) catalogued in the KEGG database, we found through literature mining that sRNAs have been reported in 44 bacteria (Supplementary Data 1 ). Of these sRNAs reported, six candidate sRNAs that had experimentally validated target binding sequences and scaffold sequences were selected: LhrA from Listeria monocytogenes 22 , BtsR1 from Bacillus thuringiensis 23 , RoxS from Bacillus subtilis 24 , Scr5239 from Streptomyces coelicolor 25 , SprX2 from Staphylococcus aureus 26 , 27 , and ArnA from C. glutamicum 28 , 29 (Fig. 1b, c , Supplementary Table 2 ).…”

Section: Resultsmentioning

confidence: 99%

Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs

et al. 2023

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Synthetic sRNAs allow knockdown of target genes at translational level, but have been restricted to a limited number of bacteria. Here, we report the development of a broad-host-range synthetic sRNA (BHR-sRNA) platform employing the RoxS scaffold and the Hfq chaperone from Bacillus subtilis. BHR-sRNA is tested in 16 bacterial species including commensal, probiotic, pathogenic, and industrial bacteria, with >50% of target gene knockdown achieved in 12 bacterial species. For medical applications, virulence factors in Staphylococcus epidermidis and Klebsiella pneumoniae are knocked down to mitigate their virulence-associated phenotypes. For metabolic engineering applications, high performance Corynebacterium glutamicum strains capable of producing valerolactam (bulk chemical) and methyl anthranilate (fine chemical) are developed by combinatorial knockdown of target genes. A genome-scale sRNA library covering 2959 C. glutamicum genes is constructed for high-throughput colorimetric screening of indigoidine (natural colorant) overproducers. The BHR-sRNA platform will expedite engineering of diverse bacteria of both industrial and medical interest.

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sRNA scr5239 Involved in Feedback Loop Regulation of Streptomyces coelicolor Central Metabolism

Cited by 8 publications

References 42 publications

A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides

A Complex Network of Sigma Factors and sRNA StsR Regulates Stress Responses in R. sphaeroides

Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds

Targeted and high-throughput gene knockdown in diverse bacteria using synthetic sRNAs

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