Two Functionally Distinct Regions Upstream of thecbbI Operon of Rhodobacter sphaeroides Regulate Gene Expression

ABSTRACT A number ofcbbFI ::lacZ translational fusion plasmids containing various lengths of sequence 5′ to the form I (cbbI ) Calvin-Benson-Bassham cycle operon (cbbFIcbbPIcbbAIcbbLIcbbSI ) of Rhodobacter sphaeroides were constructed. Expression of β-galactosidase was monitored under a variety of growth conditions. It was found that 103 bp of sequence upstream of thecbbFI transcription start was sufficient to confer low levels of regulated cbbI promoter expression; this activity was dependent on the presence of an intactcbbR gene. Additionally, R. sphaeroidesCbbR was shown to bind to the region between 9 and 100 bp 5′ to thecbbFI transcription start. Inclusion of an additional upstream sequence, from 280 to 636 bp 5′ tocbbFI , resulted in a significant increase in regulated cbbI promoter expression under all growth conditions tested. A 50-bp region responsible for the majority of this increase occurs between 280 and 330 bp 5′ tocbbFI . The additional 306 bp of upstream sequence from 330 to 636 bp also appears to play a positive regulatory role. A 4-bp deletion 281 to 284 bp 5′ to cbbFI significantly reduced cbbI expression while the proper regulatory pattern was retained. These studies provide evidence for the presence of two functionally distinct regions of thecbbI promoter, with the distal domain providing significant regulated promoter activity that adheres to the normal pattern of expression.

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Promoter activity buffering reduces the fitness cost of misregulation

10.1101/215186 ◽

2017 ◽

Author(s):

Miquel Angel Schikora-Tamarit ◽

Guillem Lopez-Grado i Salinas ◽

Carolina Gonzalez Navasa ◽

Irene Calderon ◽

Xavi Marcos-Fa ◽

...

Keyword(s):

Gene Expression ◽

Response Curve ◽

Promoter Activity ◽

Experimental System ◽

Feedback Loops ◽

Open Reading Frame ◽

Regulate Gene Expression ◽

Reading Frame ◽

Organismal Fitness ◽

Regulate Gene

Cells regulate gene expression by changing the concentration and activity of transcription factors (TFs). The response of each gene to changes in TF activity is generally assumed to be encoded in the promoter. Here we show that, even when the promoter itself remains constant, each gene has a unique TF dose response curve. Many genes have an intrinsic ability to either buffer or amplify the effects of high promoter activity. We present a coupled mathematical model and experimental system for quantifying this property. Promoter activity buffering can be encoded by sequences in both the open reading frame and 3UTR and can be implemented by both autoregulatory feedback loops and by titration of limiting trans regulators. We show experimentally that promoter activity buffering insulates cells from fitness defects due to misexpression. The response of genes to changes in [TF] is encoded by sequences outside of the promoter, and this effect can either insulate or amplify the effects of aneuploidy and misregulation on organismal fitness.

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Faculty Opinions recommendation of Gbetagamma dimers released in response to thyrotropin activate phosphoinositide 3-kinase and regulate gene expression in thyroid cells.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1105176.561368 ◽

2008 ◽

Author(s):

Sissy Jhiang

Keyword(s):

Gene Expression ◽

Thyroid Cells ◽

Regulate Gene Expression ◽

Phosphoinositide 3 Kinase ◽

Regulate Gene

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Faculty Opinions recommendation of Adipose-derived circulating miRNAs regulate gene expression in other tissues.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.727307512.793529544 ◽

2017 ◽

Author(s):

Aurelio Teleman ◽

Parthive Patel

Keyword(s):

Gene Expression ◽

Circulating Mirnas ◽

Regulate Gene Expression ◽

Regulate Gene

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Pubertal Social Isolation and Hypervigilance Regulate Gene Expression Mechanisms of Mammary Differentiation and Cancer Risks

10.21236/ada560196 ◽

2010 ◽

Author(s):

Martha McClintock

Keyword(s):

Gene Expression ◽

Social Isolation ◽

Cancer Risks ◽

Regulate Gene Expression ◽

Regulate Gene

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Human cytomegalovirus US3 and UL36-38 immediate-early proteins regulate gene expression.

Journal of Virology ◽

10.1128/jvi.66.1.95-105.1992 ◽

1992 ◽

Vol 66 (1) ◽

pp. 95-105 ◽

Cited By ~ 61

Author(s):

A M Colberg-Poley ◽

L D Santomenna ◽

P P Harlow ◽

P A Benfield ◽

D J Tenney

Keyword(s):

Gene Expression ◽

Human Cytomegalovirus ◽

Immediate Early ◽

Regulate Gene Expression ◽

Early Proteins ◽

Immediate Early Proteins ◽

Regulate Gene

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Arabidopsis heat shock transcription factor HSFA7b positively mediates salt stress tolerance by binding to an E-box-like motif to regulate gene expression

Journal of Experimental Botany ◽

10.1093/jxb/erz261 ◽

2019 ◽

Vol 70 (19) ◽

pp. 5355-5374 ◽

Cited By ~ 11

Author(s):

Dandan Zang ◽

Jingxin Wang ◽

Xin Zhang ◽

Zhujun Liu ◽

Yucheng Wang

Keyword(s):

Gene Expression ◽

Transcription Factors ◽

Heat Shock ◽

Salt Tolerance ◽

Stress Responses ◽

Ion Homeostasis ◽

Cellulose Synthase ◽

Regulate Gene Expression ◽

E Box ◽

Regulate Gene

Abstract Plant heat shock transcription factors (HSFs) are involved in heat and other abiotic stress responses. However, their functions in salt tolerance are little known. In this study, we characterized the function of a HSF from Arabidopsis, AtHSFA7b, in salt tolerance. AtHSFA7b is a nuclear protein with transactivation activity. ChIP-seq combined with an RNA-seq assay indicated that AtHSFA7b preferentially binds to a novel cis-acting element, termed the E-box-like motif, to regulate gene expression; it also binds to the heat shock element motif. Under salt conditions, AtHSFA7b regulates its target genes to mediate serial physiological changes, including maintaining cellular ion homeostasis, reducing water loss rate, decreasing reactive oxygen species accumulation, and adjusting osmotic potential, which ultimately leads to improved salt tolerance. Additionally, most cellulose synthase-like (CSL) and cellulose synthase (CESA) family genes were inhibited by AtHSFA7b; some of them were randomly selected for salt tolerance characterization, and they were mainly found to negatively modulate salt tolerance. By contrast, some transcription factors (TFs) were induced by AtHSFA7b; among them, we randomly identified six TFs that positively regulate salt tolerance. Thus, AtHSFA7b serves as a transactivator that positively mediates salinity tolerance mainly through binding to the E-box-like motif to regulate gene expression.

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Genome‐wide chromatin occupancy of BRDT and gene expression analysis suggest transcriptional partners and specific epigenetic landscapes that regulate gene expression during spermatogenesis

Molecular Reproduction and Development ◽

10.1002/mrd.23449 ◽

2021 ◽

Author(s):

Yoon Ra Her ◽

Li Wang ◽

Iouri Chepelev ◽

Marcia Manterola ◽

Binyamin Berkovits ◽

...

Keyword(s):

Gene Expression ◽

Expression Analysis ◽

Gene Expression Analysis ◽

Regulate Gene Expression ◽

Genome Wide ◽

Regulate Gene

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A First Step towards Learning which uORFs Regulate Gene Expression

Journal of Integrative Bioinformatics ◽

10.1515/jib-2006-31 ◽

2006 ◽

Vol 3 (2) ◽

pp. 109-122 ◽

Cited By ~ 1

Author(s):

◽

Christopher H. Bryant ◽

Graham J.L. Kemp ◽

Marija Cvijovic

Keyword(s):

Gene Expression ◽

Inductive Logic ◽

Preliminary Evidence ◽

Open Reading Frames ◽

Yeast Saccharomyces Cerevisiae ◽

Regulate Gene Expression ◽

Integrative System ◽

Upstream Open Reading Frames ◽

Reading Frames ◽

Regulate Gene

Summary We have taken a first step towards learning which upstream Open Reading Frames (uORFs) regulate gene expression (i.e., which uORFs are functional) in the yeast Saccharomyces cerevisiae. We do this by integrating data from several resources and combining a bioinformatics tool, ORF Finder, with a machine learning technique, inductive logic programming (ILP). Here, we report the challenge of using ILP as part of this integrative system, in order to automatically generate a model that identifies functional uORFs. Our method makes searching for novel functional uORFs more efficient than random sampling. An attempt has been made to predict novel functional uORFs using our method. Some preliminary evidence that our model may be biologically meaningful is presented.

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