A Feed-Forward Loop Consisting of the Response Regulator RpaB and the Small RNA PsrR1 Controls Light Acclimation of Photosystem I Gene Expression in the CyanobacteriumSynechocystissp. PCC 6803

ABSTRACT The coordinated high-light response of genes encoding subunits of photosystem I (PSI) is achieved by the AT-rich region located just upstream of the core promoter in Synechocystis sp. strain PCC 6803. The upstream element enhances the basal promoter activity under low-light conditions, whereas this positive regulation is lost immediately after the shift to high-light conditions. In this study, we focused on a high-light regulatory 1 (HLR1) sequence included in the upstream element of every PSI gene examined. A gel mobility shift assay revealed that a response regulator RpaB binds to the HLR1 sequence in PSI promoters. Base substitution in the HLR1 sequence or decrease in copy number of the rpaB gene resulted in decrease in the promoter activity of PSI genes under low-light conditions. These observations suggest that RpaB acts as a transcriptional activator for PSI genes. It is likely that RpaB binds to the HLR1 sequence under low-light conditions and works for positive regulation of PSI genes and for negative regulation of high-light-inducible genes depending on the location of the HLR1 sequence within target promoters.

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Small RNA driven feed-forward loop: critical role of sRNA in noise filtering

Physical Biology ◽

10.1088/1478-3975/ab1563 ◽

2019 ◽

Author(s):

Swathi Tej ◽

Kumar Gaurav ◽

Sutapa Mukherji

Keyword(s):

Small Rna ◽

Critical Role ◽

Noise Filtering ◽

Feed Forward ◽

Feed Forward Loop

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MUTE Directly Orchestrates Cell State Switch and the Single Symmetric Division to Create Stomata

10.1101/286443 ◽

2018 ◽

Cited By ~ 1

Author(s):

Soon-Ki Han ◽

Xingyun Qi ◽

Kei Sugihara ◽

Jonathan H. Dang ◽

Takaho A. Endo ◽

...

Keyword(s):

Gene Expression ◽

Cell Cycle ◽

Cell Division ◽

List Type ◽

Transcriptional Repressors ◽

Potent Inducer ◽

Feed Forward ◽

Feed Forward Loop ◽

Symmetric Division ◽

Cell Cycle Genes

SUMMARYPrecise cell division control is critical for developmental patterning. For the differentiation of a functional stoma, a cellular valve for efficient gas exchange, the single symmetric division of an immediate precursor is absolutely essential. Yet, the mechanism governing the single division event remains unclear. Here we report the complete inventories of gene expression by the Arabidopsis bHLH protein MUTE, a potent inducer of stomatal differentiation. MUTE switches the gene expression program initiated by its sister bHLH, SPEECHLESS. MUTE directly induces a suite of cell-cycle genes, including CYCD5;1, and their transcriptional repressors, FAMA and FOUR LIPS. The architecture of the regulatory network initiated by MUTE represents an Incoherent Type 1 Feed-Forward Loop. Our mathematical modeling and experimental perturbations support a notion that MUTE orchestrates a transcriptional cascade leading to the tightly-restricted, robust pulse of cell-cycle gene expression, thereby ensuring the single cell division to create functional stomata.HighlightsComplete inventories of gene expression in stomatal differentiation state are elucidatedMUTE switches stomatal patterning program initiated by its sister bHLH, SPEECHLESSMUTE directly induces cell-cycle genes and their direct transcriptional repressorsIncoherent feed-forward loop by MUTE ensures the single division of a stomatal precursor

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Maximized redundant and synergistic information transfers predict the rise in the output gene expression noise in a generic class of coherent type-1 feed-forward loop networks

10.1101/2021.09.12.459930 ◽

2021 ◽

Author(s):

Md Sorique Aziz Momin ◽

Ayan Biswas

Keyword(s):

Gene Expression ◽

Gene Product ◽

Partial Information ◽

Feed Forward ◽

Gene Expression Noise ◽

Feed Forward Loop ◽

Output Noise ◽

Generic Class ◽

Information Transfers

AbstractWe apply the partial information decomposition principle to a generic coherent type-1 feed-forward loop (C1-FFL) motif with tunable direct and indirect transcriptional regulations of the output gene product and quantify the redundant, synergistic, and unique information transfers from the regulators to their target output species. Our results which are obtained within the small-noise regime of a Gaussian framework reveal that the redundant and synergistic information transfers are antagonistically related to the output noise. Most importantly, these two information flavors are maximized prior to the minimization and subsequent growth of the output noise. Therefore, we hypothesize that the dynamic information redundancy and synergy maxima may possibly be utilized as efficient statistical predictors to forecast the increasing trend of the fluctuations associated with the output gene expression dynamics in the C1-FFL class of network motifs. Our core analytical finding is supported by exact stochastic simulation data and furthermore validated for a diversified repertoire of biologically plausible parameters. Since, the output gene product serves essential physiological purposes in the cell, a predictive estimate of its noise level is supposed to be of considerable biophysical utility.

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