Dual Promoters Control Expression of the Bacillus anthracis Virulence Factor AtxA

ABSTRACT The AtxA virulence regulator of Bacillus anthracis is required for toxin and capsule gene expression. AtxA is a phosphotransferase system regulatory domain-containing protein whose activity is regulated by phosphorylation/dephosphorylation of conserved histidine residues. Here we report that transcription of the atxA gene occurs from two independent promoters, P1 (previously described by Dai et al. [Z. Dai, J. C. Sirard, M. Mock, and T. M. Koehler, Mol. Microbiol. 16:1171-1181, 1995]) and P2, whose transcription start sites are separated by 650 bp. Both promoters have −10 and −35 consensus sequences compatible with recognition by σA-containing RNA polymerase, and neither promoter depends on the sporulation sigma factor SigH. The dual promoter activity and the extended untranslated mRNA suggest that as-yet-unknown regulatory mechanisms may act on this region to influence the level of AtxA in the cell.

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Transcription initiation mapping in 31 bovine tissues reveals complex promoter activity, pervasive transcription, and tissue-specific promoter usage

10.1101/2020.09.05.284547 ◽

2020 ◽

Author(s):

D.E. Goszczynski ◽

M.M. Halstead ◽

A.D. Islas-Trejo ◽

H. Zhou ◽

P.J. Ross

Keyword(s):

Transcription Initiation ◽

Promoter Activity ◽

Bovine Genome ◽

Transcription Start ◽

Protein Coding ◽

Tissue Specific ◽

Transcription Start Sites ◽

Expression Control ◽

Tissue Specific Promoter ◽

Genome Annotations

ABSTRACTCharacterizing transcription start sites is essential for understanding the regulatory mechanisms that control gene expression. Recently, a new bovine genome assembly (ARS-UCD1.2) with high continuity, accuracy, and completeness was released; however, the functional annotation of the bovine genome lacks precise transcription start sites and includes a low number of transcripts in comparison to human and mouse. Using the RAMPAGE approach, this study identified transcription start sites at high resolution in a large collection of bovine tissues. We found several known and novel transcription start sites attributed to promoters of protein coding and lncRNA genes that were validated through experimental and in silico evidence. With these findings, the annotation of transcription start sites in cattle reached a level comparable to the mouse and human genome annotations. In addition, we identified and characterized transcription start sites for antisense transcripts derived from bidirectional promoters, potential lncRNAs, mRNAs, and pre-miRNAs. We also analyzed the quantitative aspects of RAMPAGE data for producing a promoter activity atlas, reaching highly reproducible results comparable to traditional RNA-Seq. Lastly, gene co-expression networks revealed an impressive use of tissue-specific promoters, especially between brain and testicle, which expressed several genes in common from alternate transcription start sites. Regions surrounding co-expressed modules were enriched in binding factor motifs representative of their tissues. This annotation will be highly useful for future studies on expression control in cattle and other species. Furthermore, these data provide significant insight into transcriptional activity for a comprehensive set of tissues.

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The Promoter of the Yeast INO4Regulatory Gene: a Model of the Simplest Yeast Promoter

Journal of Bacteriology ◽

10.1128/jb.182.10.2746-2752.2000 ◽

2000 ◽

Vol 182 (10) ◽

pp. 2746-2752 ◽

Cited By ~ 12

Author(s):

Kelly A. Robinson ◽

John M. Lopes

Keyword(s):

Promoter Activity ◽

Small Region ◽

Transcription Start ◽

Additional Element ◽

S1 Nuclease ◽

Activator Proteins ◽

Transcription Start Sites ◽

S1 Nuclease Mapping ◽

Nuclease Mapping ◽

Yeast Genes

ABSTRACT In Saccharomyces cerevisiae, the phospholipid biosynthetic genes are transcriptionally regulated in response to inositol and choline. This regulation requires the transcriptional activator proteins Ino4p and Ino2p, which form a heterodimer that binds to the UAS INO element. We have previously shown that the promoters of the INO4 and INO2 genes are among the weakest promoters characterized in yeast. Because little is known about the promoters of weakly expressed yeast genes, we report here the analysis of the constitutive INO4 promoter. Promoter deletion constructs scanning 1,000 bp upstream of theINO4 gene identified a small region (−58 to −46) that is absolutely required for expression. S1 nuclease mapping shows that this region contains the transcription start sites for the INO4gene. An additional element (−114 to −86) modestly enhancesINO4 promoter activity (fivefold). Thus, the region required for INO4 transcription is limited to 68 bp. These studies also found that INO4 gene expression is not autoregulated by Ino2p and Ino4p, despite the presence of a putative UAS INO element in the INO4promoter. We further report that the INO4 steady-state transcript levels and Ino4p levels are regulated twofold in response to inositol and choline, suggesting a posttranscriptional mechanism of regulation.

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The TetR-Type Transcriptional Repressor RolR from Corynebacterium glutamicum Regulates Resorcinol Catabolism by Binding to a Unique Operator,rolO

Applied and Environmental Microbiology ◽

10.1128/aem.01304-12 ◽

2012 ◽

Vol 78 (17) ◽

pp. 6009-6016 ◽

Cited By ~ 11

Author(s):

Tang Li ◽

Kexin Zhao ◽

Yan Huang ◽

Defeng Li ◽

Cheng-Ying Jiang ◽

...

Keyword(s):

Corynebacterium Glutamicum ◽

Promoter Activity ◽

Activity Analysis ◽

Inverted Repeats ◽

Catabolic Pathway ◽

Transcription Start ◽

Content Type ◽

Transcription Start Sites ◽

Reverse Transcription Pcr ◽

Promoter Activity Analysis

ABSTRACTTherol(designated forresorcinol) gene clusterrolRHMDis involved in resorcinol catabolism inCorynebacterium glutamicum, and RolR is the TetR-type regulator. In this study, we investigated how RolR regulated the transcription of therolgenes inC. glutamicum. The transcription start sites and promoters ofrolRandrolHMDwere identified. Quantitative reverse transcription-PCR and promoter activity analysis indicated that RolR negatively regulated the transcription ofrolHMDand of its own gene. Further, a 29-bp operatorrolOwas located at the intergenic region ofrolRandrolHMDand was identified as the sole binding site for RolR. It contained two overlapping inverted repeats and they were essential for RolR-binding. The binding of RolR torolOwas affected by resorcinol and hydroxyquinol, which are the starting compounds of resorcinol catabolic pathway. These two compounds were able to dissociate RolR-rolOcomplex, thus releasing RolR from the complex and derepressing the transcription ofrolgenes inC. glutamicum. It is proposed that the binding of RolR to its operatorrolOblocks the transcription ofrolHMDand of its own gene, thus negatively regulated resorcinol degradation inC. glutamicum.

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Promoter sequence and architecture determine expression variability and confer robustness to genetic variants

10.1101/2021.10.29.466407 ◽

2021 ◽

Author(s):

Hjorleifur Einarsson ◽

Marco Salvatore ◽

Christian Vaagenso ◽

Nicolas Alcaraz ◽

Jette Bornholdt Lange ◽

...

Keyword(s):

Genetic Variants ◽

Binding Sites ◽

Promoter Sequence ◽

Effect Sizes ◽

Regulatory Mechanisms ◽

Transcription Start ◽

Mutational Robustness ◽

Expression Variability ◽

Transcription Start Sites ◽

The Relationship

Genetic and environmental exposures cause variability in gene expression. Although most genes are affected in a population, their effect sizes vary greatly, indicating the existence of regulatory mechanisms that could amplify or attenuate expression variability. Here, we investigate the relationship between the sequence and transcription start site architectures of promoters and their expression variability across human individuals. We find that expression variability is largely determined by a promoter's DNA sequence and its binding sites for specific transcription factors. We further demonstrate that flexible usage of transcription start sites within a promoter attenuates variability, providing transcriptional and mutational robustness.

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Transcriptional Analysis of the Bacillus anthracis Capsule Regulators

Journal of Bacteriology ◽

10.1128/jb.187.15.5108-5114.2005 ◽

2005 ◽

Vol 187 (15) ◽

pp. 5108-5114 ◽

Cited By ~ 45

Author(s):

Melissa Drysdale ◽

Agathe Bourgogne ◽

Theresa M. Koehler

Keyword(s):

Bacillus Anthracis ◽

Double Mutant ◽

Current Model ◽

Positive Control ◽

Transcriptional Analysis ◽

Start Site ◽

Transcription Start ◽

Positive Regulation ◽

Transcription Start Sites ◽

Gene Transcripts

ABSTRACT The poly-d-glutamic acid capsule of Bacillus anthracis is essential for virulence. Control of capsule synthesis occurs at the level of transcription and involves positive regulation of the capsule biosynthetic operon capBCAD by a CO2/bicarbonate signal and three plasmid-borne regulators: atxA, acpA, and acpB. Although the molecular mechanism for control of cap transcription is unknown, atxA affects cap expression via positive control of acpA and acpB, two genes with partial functional similarity. Transcriptional analyses of a genetically complete strain indicate that capB expression is several hundred-fold higher during growth in 5% CO2 compared to growth in air. atxA was expressed appreciably during growth in air and induced only 2.5-fold by CO2. In contrast, expression of acpA and acpB was induced up to 23-fold and 59-fold, respectively, by CO2. The 5′-end mapping of gene transcripts revealed atxA-regulated and atxA-independent apparent transcription start sites for capB, acpA, and acpB. Transcripts mapping to all atxA-regulated start sites were increased during growth in elevated CO2. The acpA gene has one atxA-regulated and one atxA-independent start site. acpB lies downstream of capBCAD. A single atxA-independent start site maps immediately upstream of acpB. atxA-mediated control of acpB appears to occur via transcriptional read-through from atxA-dependent start sites 5′ of capB. One atxA-independent and two atxA-regulated start sites map upstream of capB. Transcription from the atxA-regulated start sites of capBCAD was reduced significantly in an acpA acpB double mutant but unaffected in mutants with deletion of only acpA or acpB, in agreement with the current model for epistatic relationships between the regulators.

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