Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

Lee, Yong Jae; Lee, Namil; Hwang, Soonkyu; Kim, Woori; Jeong, Yu‐Jin; Cho, Suhyung; Kim, Jaehyung; Cho, Byung-Kwan

doi:10.1038/s41597-020-00775-w

Cited by 9 publications

(11 citation statements)

References 32 publications

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“…The 3′ end of Str13 was then determined by 3′ RACE ( Figure 2E ) at the position 3,934,920, which corresponds to the 3′ end of scr3559 ( Vockenhuber et al, 2011 ; Moody et al, 2013 ) but not ssrS/6S RNA. The 3′ end in the same position (3,934,920) was identified also by Term-seq ( Lee et al, 2020 ).…”

Section: Resultsmentioning

confidence: 89%

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

et al. 2022

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Bacteria employ small non-coding RNAs (sRNAs) to regulate gene expression. Ms1 is an sRNA that binds to the RNA polymerase (RNAP) core and affects the intracellular level of this essential enzyme. Ms1 is structurally related to 6S RNA that binds to a different form of RNAP, the holoenzyme bearing the primary sigma factor. 6S RNAs are widespread in the bacterial kingdom except for the industrially and medicinally important Actinobacteria. While Ms1 RNA was identified in Mycobacterium, it is not clear whether Ms1 RNA is present also in other Actinobacteria species. Here, using a computational search based on secondary structure similarities combined with a linguistic gene synteny approach, we identified Ms1 RNA in Streptomyces. In S. coelicolor, Ms1 RNA overlaps with the previously annotated scr3559 sRNA with an unknown function. We experimentally confirmed that Ms1 RNA/scr3559 associates with the RNAP core without the primary sigma factor HrdB in vivo. Subsequently, we applied the computational approach to other Actinobacteria and identified Ms1 RNA candidates in 824 Actinobacteria species, revealing Ms1 RNA as a widespread class of RNAP binding sRNAs, and demonstrating the ability of our multifactorial computational approach to identify weakly conserved sRNAs in evolutionarily distant genomes.

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Section: Resultsmentioning

confidence: 89%

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

et al. 2022

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“…On the other hand, Term-Seq reveals the 3′-ends of transcripts, including transcription termination sites and processed 3′-ends. Those information-rich data sets, regulatory elements identified from the TU architecture along with gene expression data, will enable expanding our knowledge of comprehensive genetic regulatory features in S. avermitilis via integrated data analysis [19][20][21][22][23][24].…”

Section: Introductionmentioning

confidence: 99%

Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information

Lee

Hwang

et al. 2022

BMC Genomics

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Background The gram-positive bacterium, Streptomyces avermitilis, holds industrial importance as the producer of avermectin, a widely used anthelmintic agent, and a heterologous expression host of secondary metabolite-biosynthetic gene clusters. Despite its industrial importance, S. avermitilis’ genome organization and regulation of gene expression remain poorly understood. In this study, four different types of Next-Generation Sequencing techniques, including dRNA-Seq, Term-Seq, RNA-Seq and ribosome profiling, were applied to S. avermitilis to determine transcription units of S. avermitilis at a genome-wide level and elucidate regulatory elements for transcriptional and translational control of individual transcription units. Result By applying dRNA-Seq and Term-Seq to S. avermitilis MA-4680, a total of 2361 transcription start sites and 2017 transcript 3′-end positions were identified, respectively, leading to determination of 1601 transcription units encoded in S. avermitilis’ genome. Cataloguing the transcription units and integrated analysis of multiple high-throughput data types revealed the presence of diverse regulatory elements for gene expression, such as promoters, 5′-UTRs, terminators, 3′-UTRs and riboswitches. The conserved promoter motifs were identified from 2361 transcription start sites as 5′-TANNNT and 5′-BTGACN for the − 10 and − 35 elements, respectively. The − 35 element and spacer lengths between − 10 and − 35 elements were critical for transcriptional regulation of functionally distinct genes, suggesting the involvement of unique sigma factors. In addition, regulatory sequences recognized by antibiotic regulatory proteins were identified from the transcription start site information. Analysis of the 3′-end of RNA transcript revealed that stem structure formation is a major determinant for transcription termination of most transcription units. Conclusions The transcription unit architecture elucidated from the transcripts’ boundary information provides insights for unique genetic regulatory mechanisms of S. avermitilis. Our findings will elevate S. avermitilis’ potential as a production host for a diverse set of secondary metabolites.

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“…For example, S. coelicolor A3(2) contains 23 gene clusters (accounting for 5% of all genes) and S. avermitilis contains 30 gene clusters (6.6% of all genes), which were believed to be acquired through horizontal gene transfer. 9,10 Streptomyces is a powerful chassis for natural product production and genetic manipulation. On the one hand, exible regions of Streptomyces can be modied, for example by deletion of large segments to simplify modied strains with less energy consumption and a shorter life cycle.…”

Section: Streptomycesmentioning

confidence: 99%

Structural diversity, biosynthesis, and biological functions of lipopeptides fromStreptomyces

et al. 2023

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Genome-scale determination of 5´ and 3´ boundaries of RNA transcripts in Streptomyces genomes

Cited by 9 publications

References 32 publications

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

Ms1 RNA Interacts With the RNA Polymerase Core in Streptomyces coelicolor and Was Identified in Majority of Actinobacteria Using a Linguistic Gene Synteny Search

Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information

Structural diversity, biosynthesis, and biological functions of lipopeptides fromStreptomyces

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