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

Abstract 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. avermit...

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Main Authors: Yongjae Lee, Namil Lee, Soonkyu Hwang, Woori Kim, Suhyung Cho, Bernhard O. Palsson, Byung-Kwan Cho
Format: Article
Language:English
Published: BMC 2022-01-01
Series:BMC Genomics
Subjects:
Online Access:https://doi.org/10.1186/s12864-022-08314-0
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author Yongjae Lee
Namil Lee
Soonkyu Hwang
Woori Kim
Suhyung Cho
Bernhard O. Palsson
Byung-Kwan Cho
author_facet Yongjae Lee
Namil Lee
Soonkyu Hwang
Woori Kim
Suhyung Cho
Bernhard O. Palsson
Byung-Kwan Cho
author_sort Yongjae Lee
collection DOAJ
description Abstract 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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spelling doaj.art-51a15320dff34668977923c340523c7d2022-12-21T19:44:11ZengBMCBMC Genomics1471-21642022-01-0123111610.1186/s12864-022-08314-0Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary informationYongjae Lee0Namil Lee1Soonkyu Hwang2Woori Kim3Suhyung Cho4Bernhard O. Palsson5Byung-Kwan Cho6Department of Biological Sciences, Korea Advanced Institute of Science and TechnologyDepartment of Biological Sciences, Korea Advanced Institute of Science and TechnologyDepartment of Biological Sciences, Korea Advanced Institute of Science and TechnologyDepartment of Biological Sciences, Korea Advanced Institute of Science and TechnologyDepartment of Biological Sciences, Korea Advanced Institute of Science and TechnologyDepartment of Bioengineering, University of California San DiegoDepartment of Biological Sciences, Korea Advanced Institute of Science and TechnologyAbstract 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.https://doi.org/10.1186/s12864-022-08314-0Streptomyces avermitilisTranscription unit architectureRegulatory elements
spellingShingle Yongjae Lee
Namil Lee
Soonkyu Hwang
Woori Kim
Suhyung Cho
Bernhard O. Palsson
Byung-Kwan Cho
Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information
BMC Genomics
Streptomyces avermitilis
Transcription unit architecture
Regulatory elements
title Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information
title_full Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information
title_fullStr Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information
title_full_unstemmed Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information
title_short Genome-scale analysis of genetic regulatory elements in Streptomyces avermitilis MA-4680 using transcript boundary information
title_sort genome scale analysis of genetic regulatory elements in streptomyces avermitilis ma 4680 using transcript boundary information
topic Streptomyces avermitilis
Transcription unit architecture
Regulatory elements
url https://doi.org/10.1186/s12864-022-08314-0
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