Title: RIViT-seq enables systematic identification of regulons of transcriptional machineries

Journal Article · · Nature Communications
ORCiD logo; ORCiD logo

Abstract Transcriptional regulation is a critical process to ensure expression of genes necessary for growth and survival in diverse environments. Transcription is mediated by multiple transcription factors including activators, repressors and sigma factors. Accurate computational prediction of the regulon of target genes for transcription factors is difficult and experimental identification is laborious and not scalable. Here, we demonstrate regulon identification by in vitro transcription-sequencing (RIViT-seq) that enables systematic identification of regulons of transcription factors by combining an in vitro transcription assay and RNA-sequencing. Using this technology, target genes of 11 sigma factors were identified in Streptomyces coelicolor A3(2). The RIViT-seq data expands the transcriptional regulatory network in this bacterium, discovering regulatory cascades and crosstalk between sigma factors. Implementation of RIViT-seq with other transcription factors and in other organisms will improve our understanding of transcriptional regulatory networks across biology.

Research Organization:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Organization:
USDOE; USDOE Office of Science (SC)
Grant/Contract Number:
AC02-05CH11231
OSTI ID:
1872803
Journal Information:
Nature Communications, Journal Name: Nature Communications Journal Issue: 1 Vol. 13; ISSN 2041-1723
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United Kingdom
Language:
English

References (50)

Defining the Bacillus subtilis σW regulon: a comparative analysis of promoter consensus search, run-off transcription/macroarray analysis (ROMA), and transcriptional profiling approaches journal February 2002
Cascade of sigma factors in streptomycetes: identification of a new extracytoplasmic function sigma factor σJ that is under the control of the stress-response sigma factor σH in Streptomyces coelicolor A3(2) journal August 2006
Post-transcriptional Regulation of the Streptomyces coelicolor Stress Responsive Sigma Factor, SigH, Involves Translational Control, Proteolytic Processing, and an Anti-sigma Factor Homolog journal January 2003
The ECF σ factor RpoI of R. leguminosarum initiates transcription of the vbsGSO and vbsADL siderophore biosynthetic genes in vitro journal June 2003
Regulation of an alternative sigma factor σI by a partner switching mechanism with an anti-sigma factor PrsI and an anti-anti-sigma factor ArsI in Streptomyces coelicolor A3(2) journal January 2012
The σF-specific anti-sigma factor RsfA is one of the protein kinases that phosphorylates the pleiotropic anti-anti-sigma factor BldG in Streptomyces coelicolor A3(2) journal April 2014
Pleiotropic anti-anti-sigma factor BldG is phosphorylated by several anti-sigma factor kinases in the process of activating multiple sigma factors in Streptomyces coelicolor A3(2) journal September 2020
Regulation of bacterial RNA polymerase σ factor activity: a structural perspective journal April 2008
c-di-GMP Arms an Anti-σ to Control Progression of Multicellular Differentiation in Streptomyces journal February 2020
Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) journal May 2002
Normalization of RNA-seq data using factor analysis of control genes or samples journal August 2014
The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2) journal June 2016
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype journal August 2019
Functional characterization of the principal sigma factor RpoD of phytoplasmas via an in vitro transcription assay journal July 2015
Induction of a stable sigma factor SigR by translation-inhibiting antibiotics confers resistance to antibiotics journal June 2016
Defining the disulphide stress response in Streptomyces coelicolor A3(2): identification of the sigmaR regulon journal November 2001
Specialized osmotic stress response systems involve multiple SigB-like sigma factors in Streptomyces coelicolor: Osmotic stress response systems in S. coelicolor journal January 2003
The Sequence Alignment/Map format and SAMtools journal June 2009
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features journal November 2013
sigma R, an RNA polymerase sigma factor that modulates expression of the thioredoxin system in response to oxidative stress in Streptomyces coelicolor A3(2) journal October 1998
Identification of sigma factors for growth phase-related promoter selectivity of RNA polymerases from Streptomyces coelicolor A3(2) journal July 1997
Lysine acetylation of the housekeeping sigma factor enhances the activity of the RNA polymerase holoenzyme journal January 2020
Identification of the CRP regulon using in vitro and in vivo transcriptional profiling journal October 2004
MEME SUITE: tools for motif discovery and searching journal May 2009
In vitro transcription profiling of the σ S subunit of bacterial RNA polymerase: re-definition of the σ S regulon and identification of σ S -specific promoter sequence elements journal March 2011
Mycobacterium tuberculosis RbpA protein is a new type of transcriptional activator that stabilizes the σ A -containing RNA polymerase holoenzyme journal May 2012
Pfam: the protein families database journal November 2013
The actinobacterial transcription factor RbpA binds to the principal sigma subunit of RNA polymerase journal April 2013
DNA mapping and kinetic modeling of the HrdB regulon in Streptomyces coelicolor journal October 2018
Evolution of the extracytoplasmic function σ factor protein family journal January 2020
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 journal March 2010
In vitro transcription analysis by reconstituted cyanobacterial RNA polymerase: roles of group 1 and 2 sigma factors and a core subunit, RpoC2: Roles of cyanobacterial sigma factors & RpoC2 journal November 2004
Expression of the chaplin and rodlin hydrophobic sheath proteins in Streptomyces venezuelae is controlled by σBldN and a cognate anti-sigma factor, RsbN: Regulation of the chaplin genes in Streptomyces journal May 2012
Conservation of thiol-oxidative stress responses regulated by SigR orthologues in actinomycetes: Conserved thiol-oxidative stress in actinomycetes journal June 2012
An alternative sigma factor governs the principal sigma factor in Streptomyces griseus: Regulation of the principal σ factor in S. griseus journal February 2013
Defining the regulon of genes controlled by σ E , a key regulator of the cell envelope stress response in Streptomyces coelicolor journal April 2019
The role of C‐terminal extensions in controlling ECF σ factor activity in the widely conserved groups ECF41 and ECF42 journal June 2019
General Pathway for Turning on Promoters Transcribed by RNA Polymerases Containing Alternative σ Factors journal July 2006
The Anti-Anti-Sigma Factor BldG Is Involved in Activation of the Stress Response Sigma Factor σ H in Streptomyces coelicolor A3(2) journal November 2010
Developmental Regulation of Transcription of whiE , a Locus Specifying the Polyketide Spore Pigment in Streptomyces coelicolor A3(2) journal May 1998
The Streptomyces coelicolor Developmental Transcription Factor σ BldN Is Synthesized as a Proprotein journal April 2003
The Bacillus subtilis Extracytoplasmic-Function σ X Factor Regulates Modification of the Cell Envelope and Resistance to Cationic Antimicrobial Peptides journal February 2004
Light-Induced Carotenogenesis in Streptomyces coelicolor A3(2): Identification of an Extracytoplasmic Function Sigma Factor That Directs Photodependent Transcription of the Carotenoid Biosynthesis Gene Cluster journal March 2005
Cloning, disruption, and transcriptional analysis of three RNA polymerase sigma factor genes of Streptomyces coelicolor A3(2) journal June 1990
redD and actII-ORF4, pathway-specific regulatory genes for antibiotic production in Streptomyces coelicolor A3(2), are transcribed in vitro by an RNA polymerase holoenzyme containing sigma hrdD journal June 1996
Global Chromosome Topology and the Two-Component Systems in Concerted Manner Regulate Transcription in Streptomyces journal December 2021
Bacterial Sigma Factors: A Historical, Structural, and Genomic Perspective journal September 2014
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 journal December 2014
Connecting Metabolic Pathways: Sigma Factors in Streptomyces spp. journal December 2017
The Stress-Responsive Alternative Sigma Factor SigB of Bacillus subtilis and Its Relatives: An Old Friend With New Functions journal September 2020

Similar Records

Related Subjects

59 BASIC BIOLOGICAL SCIENCES