Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

A majority of Rhodobacter sphaeroides promoters lack a crucial RNA polymerase recognition feature, enabling coordinated transcription activation

Journal Article · · Proceedings of the National Academy of Sciences of the United States of America
 [1];  [2];  [2];  [2];  [2];  [2];  [2];  [2]
  1. Univ. of Wisconsin, Madison, WI (United States); University of Wisconsin-Madison Department of Bacteriology
  2. Univ. of Wisconsin, Madison, WI (United States)
+ Show Author Affiliations
Using an in vitro transcription system with purified RNA polymerase (RNAP) to investigate rRNA synthesis in the photoheterotrophic α-proteobacterium Rhodobacter sphaeroides, we identified a surprising feature of promoters recognized by the major holoenzyme. Transcription from R. sphaeroides rRNA promoters was unexpectedly weak, correlating with absence of 7T, the very highly conserved thymine found at the last position in –10 elements of promoters in most bacterial species. Thymine substitutions for adenine at position –7 in the three rRNA promoters strongly increased intrinsic promoter activity, indicating that R. sphaeroides RNAP can utilize –7T when present. rRNA promoters were activated by purified R. sphaeroides CarD, a transcription factor found in many bacterial species but not in β- and γ-proteobacteria. Overall, CarD increased the activity of 15 of 16 native R. sphaeroides promoters tested in vitro that lacked –7T, whereas it had no effect on three of the four native promoters that contained –7T. Genome-wide bioinformatic analysis of promoters from R. sphaeroides and two other α-proteobacterial species indicated that 30 to 43% contained –7T, whereas 90 to 99% of promoters from non–α-proteobacteria contained –7T. Thus, promoters lacking –7T appear to be widespread in α-proteobacteria and may have evolved away from consensus to enable their coordinated regulation by transcription factors like CarD. We observed a strong reduction in R. sphaeroides CarD levels when cells enter stationary phase, suggesting that reduced activation by CarD may contribute to inhibition of rRNA transcription when cells enter stationary phase, the stage of growth when bacterial ribosome synthesis declines.
Research Organization:
Great Lakes Bioenergy Research Center, Madison, WI (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
SC0018409
OSTI ID:
1764723
Journal Information:
Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Issue: 47 Vol. 117; ISSN 0027-8424
Publisher:
National Academy of SciencesCopyright Statement
Country of Publication:
United States
Language:
English

References (55)

E.coli Fis protein activates ribosomal RNA transcription in vitro and in vivo. journal November 1990
Cell Replication Rates and Processes Concerning Antibody Productionin VitroAre Not Influenced by 2.45-GHz Microwaves at Physiologically Normal Temperatures journal June 1998
Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum journal July 1994
rRNA Promoter Regulation by Nonoptimal Binding of σ Region 1.2: An Additional Recognition Element for RNA Polymerase journal June 2006
CarD Is an Essential Regulator of rRNA Transcription Required for Mycobacterium tuberculosis Persistence journal July 2009
Structural Basis for Promoter −10 Element Recognition by the Bacterial RNA Polymerase σ Subunit journal December 2011
Genome-wide mapping of the distribution of CarD, RNAP σA, and RNAP β on the Mycobacterium smegmatis chromosome using chromatin immunoprecipitation sequencing journal December 2014
Stepwise Promoter Melting by Bacterial RNA Polymerase journal April 2020
The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2) journal June 2016
Advances in bacterial promoter recognition and its control by factors that do not bind DNA journal June 2008
Structures of an RNA polymerase promoter melting intermediate elucidate DNA unwinding journal January 2019
Caulobacter crescentus CdnL is a non-essential RNA polymerase-binding protein whose depletion impairs normal growth and rRNA transcription journal February 2017
Structure and function of CarD, an essential mycobacterial transcription factor journal July 2013
The calculation of transcript flux ratios reveals single regulatory mechanisms capable of activation and repression journal November 2018
Genome-wide effects on Escherichia coli transcription from ppGpp binding to its two sites on RNA polymerase journal April 2019
CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis journal June 2019
Identification of an UP element consensus sequence for bacterial promoters journal August 1998
A Consensus Adenine at Position –11 of the Nontemplate Strand of Bacterial Promoter Is Important for Nucleation of Promoter Melting journal March 2006
Localization and structural analysis of the ribosomal RNA operons of Rhodobacter sphaeroides journal January 1990
Anatomy of Escherichia coli σ 70 promoters journal December 2006
CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD journal April 2010
Structural basis for the bacterial transcription-repair coupling factor/RNA polymerase interaction journal August 2010
Mycobacterial RNA polymerase forms unstable open promoter complexes that are stabilized by CarD journal December 2014
CarD stabilizes mycobacterial open complexes via a two-tiered kinetic mechanism journal February 2015
A Requirement for Sodium in the Growth of Rhodopseudomonas spheroides journal June 1960
Promoter prediction in the rhizobia journal June 2006
WebLogo: A Sequence Logo Generator journal May 2004
Structural Basis of Transcription Initiation journal October 2012
A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase journal November 1993
The Core and Holoenzyme Forms of RNA Polymerase from Mycobacterium smegmatis journal November 2018
Interaction of CarD with RNA Polymerase Mediates Mycobacterium tuberculosis Viability, Rifampin Resistance, and Pathogenesis journal August 2012
Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli journal September 2014
Control of rRNA and tRNA syntheses in Escherichia coli by guanosine tetraphosphate. journal January 1982
Genome-Wide Identification of Transcription Start Sites in Two Alphaproteobacteria , Rhodobacter sphaeroides 2.4.1 and Novosphingobium aromaticivorans DSM 12444 journal September 2020
Hierarchies of base pair preferences in the P22 ant promoter. journal January 1991
Identification of cis-acting regulatory regions upstream of the rRNA operons of Rhodobacter sphaeroides. journal January 1993
Transcription properties of RNA polymerase holoenzymes isolated from the purple nonsulfur bacterium Rhodobacter sphaeroides. journal January 1993
A consensus promoter sequence for Caulobacter crescentus genes involved in biosynthetic and housekeeping functions. journal January 1995
The NtrYX Two-Component System Regulates the Bacterial Cell Envelope journal May 2020
A Rhodobacter sphaeroides Protein Mechanistically Similar to Escherichia coli DksA Regulates Photosynthetic Growth journal April 2014
Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides journal June 2017
Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters journal July 2020
Transcriptional Responses to ppGpp and DksA journal September 2018
Postgenomic Adventures with Rhodobacter sphaeroides journal October 2007
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021 journal January 2013
Global insights into energetic and metabolic networks in Rhodobacter sphaeroides journal January 2013
Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315 journal October 2015
The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle journal January 2015
Global Analysis of Photosynthesis Transcriptional Regulatory Networks journal December 2014
The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter journal January 2020
Structural Insights into RNA Polymerase Recognition and Essential Function of Myxococcus xanthus CdnL journal October 2014
Transcriptome Landscape of Mycobacterium smegmatis journal December 2017
Initial Events in Bacterial Transcription Initiation journal May 2015
CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex journal September 2015
Structure and function of the mycobacterial transcription initiation complex with the essential regulator RbpA journal January 2017

Similar Records

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex
Journal Article · Mon Sep 07 20:00:00 EDT 2015 · eLife · OSTI ID:1233324
The essential Rhodobacter sphaeroides CenKR two-component system regulates cell division and envelope biosynthesis
Journal Article · Tue Jun 28 20:00:00 EDT 2022 · PLoS Genetics · OSTI ID:1875739

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
CarD
RNA polymerase
Rhodobacter sphaeroides
promoter
−10 element