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

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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Molecular characterization, expression patterns, and promoter activity analysis of PGM1 in pigs

Genetics and Molecular Research ◽

10.4238/2015.march.31.12 ◽

2015 ◽

Vol 14 (1) ◽

pp. 2816-2824

Author(s):

J.Y. Yu ◽

S.M. Shao ◽

Y.Z. Xiong

Keyword(s):

Molecular Characterization ◽

Promoter Activity ◽

Expression Patterns ◽

Activity Analysis ◽

Promoter Activity Analysis

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Influence of cis Element Arrangement on Promoter Strength in Trichoderma reesei

Applied and Environmental Microbiology ◽

10.1128/aem.01742-17 ◽

2017 ◽

Vol 84 (1) ◽

Cited By ~ 12

Author(s):

Daniel P. Kiesenhofer ◽

Robert L. Mach ◽

Astrid R. Mach-Aigner

Keyword(s):

Trichoderma Reesei ◽

Transcription Start Site ◽

Binding Sites ◽

Inverted Repeat ◽

Promoter Activity ◽

Promoter Strength ◽

Start Site ◽

Transcription Start ◽

Content Type ◽

Sheer Number

ABSTRACTTrichoderma reeseican produce up to 100 g/liter of extracellular proteins. The major and industrially relevant products are cellobiohydrolase I (CBHI) and the hemicellulase XYNI. The genes encoding both enzymes are transcriptionally activated by the regulatory protein Xyr1. The first 850 nucleotides of thecbh1promoter contain 14 Xyr1-binding sites (XBS), and 8 XBS are present in thexyn1promoter. Some of these XBS are arranged in tandem and others as inverted repeats. One suchciselement, an inverted repeat, plays a crucial role in the inducibility of thexyn1promoter. We investigated the impact of the properties of suchciselements by shuffling them by insertion, exchange, deletion, and rearrangement ofciselements in both thecbh1andxyn1promoter. A promoter-reporter assay using theAspergillus nigergoxAgene allowed us to measure changes in the promoter strength and inducibility. Most strikingly, we found that an inverted repeat of XBS causes an important increase incbh1promoter strength and allows induction by xylan or wheat straw. Furthermore, evidence is provided that the distances ofciselements to the transcription start site have important influence on promoter activity. Our results suggest that the arrangement and distances ofciselements have large impacts on the strength of thecbh1promoter, whereas the sheer number of XBS has only secondary importance. Ultimately, the biotechnologically importantcbh1promoter can be improved byciselement rearrangement.IMPORTANCEIn the present study, we demonstrate that the arrangement ofciselements has a major impact on promoter strength and inducibility. We discovered an influence on promoter activity by the distances ofciselements to the transcription start site. Furthermore, we found that the configuration ofciselements has a greater effect on promoter strength than does the sheer number of transactivator binding sites present in the promoter. Altogether, the arrangement ofciselements is an important factor that should not be overlooked when enhancement of gene expression is desired.

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Characterization of NtREL1, a novel root-specific gene from tobacco, and upstream promoter activity analysis in homologous and heterologous hosts

Plant Cell Reports ◽

10.1007/s00299-015-1918-2 ◽

2016 ◽

Vol 35 (4) ◽

pp. 757-769 ◽

Cited By ~ 6

Author(s):

Chong Zhang ◽

Shufang Pan ◽

Hua Chen ◽

Tiecheng Cai ◽

Chunhong Zhuang ◽

...

Keyword(s):

Promoter Activity ◽

Activity Analysis ◽

Specific Gene ◽

Upstream Promoter ◽

Promoter Activity Analysis

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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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