An RpaA-Dependent Sigma Factor Cascade Sets the Timing of Circadian Transcriptional Rhythms in Synechococcus elongatus.

The circadian clock of the cyanobacterium Synechococcus elongatus PCC 7942 drives oscillations in global mRNA abundances with 24-hr periodicity under constant light conditions. The circadian clock-regulated transcription factor RpaA controls the timing of circadian gene expression, but the mechanisms underlying this control are not well understood. Here, we show that four RpaA-dependent sigma factors-RpoD2, RpoD6, RpoD5, and SigF2-are sequentially activated downstream of active RpaA and are required for proper expression of circadian mRNAs.

Dynamical localization of a thylakoid membrane binding protein is required for acquisition of photosynthetic competency.

Vipp1 is highly conserved and essential for photosynthesis, but its function is unclear as it does not participate directly in light-dependent reactions. We analyzed Vipp1 localization in live cyanobacterial cells and show that Vipp1 is highly dynamic, continuously exchanging between a diffuse fraction that is uniformly distributed throughout the cell and a punctate fraction that is concentrated at high curvature regions of the thylakoid located at the cell periphery. Experimentally perturbing the spatial distribution of Vipp1 by relocalizing it to the nucleoid causes a severe growth defect during the transition from non-photosynthetic (dark) to photosynthetic (light) growth.

An Unstable Singularity Underlies Stochastic Phasing of the Circadian Clock in Individual Cyanobacterial Cells.

The endogenous circadian clock synchronizes with environmental time by appropriately resetting its phase in response to external cues. Of note, some resetting stimuli induce attenuated oscillations of clock output, which has been observed at the population-level in several organisms and in studies of individual humans. To investigate what is happening in individual cellular clocks, we studied the unicellular cyanobacterium S.

Cyanobacteria Maintain Constant Protein Concentration despite Genome Copy-Number Variation.

The cyanobacterium Synechococcus elongatus PCC 7942 has multiple copies of its single chromosome, and the copy number varies in individual cells, providing an ideal system to study the effect of genome copy-number variation on cell size and gene expression. Using single-cell fluorescence imaging, we found that protein concentration remained constant across individual cells regardless of genome copy number. Cell volume and the total protein amount from a single gene were both positively, linearly correlated with genome copy number, suggesting that changes in cell volume play an important role in buffering genome copy-number variance.

Large-Effect Beneficial Synonymous Mutations Mediate Rapid and Parallel Adaptation in a Bacterium.

Contrary to previous understanding, recent evidence indicates that synonymous codon changes may sometimes face strong selection. However, it remains difficult to generalize the nature, strength, and mechanism(s) of such selection. Previously, we showed that synonymous variants of a key enzyme-coding gene (fae) of Methylobacterium extorquens AM1 decreased enzyme production and reduced fitness dramatically.

Circadian control of global gene expression by the cyanobacterial master regulator RpaA.

The cyanobacterial circadian clock generates genome-wide transcriptional oscillations and regulates cell division, but the underlying mechanisms are not well understood. Here, we show that the response regulator RpaA serves as the master regulator of these clock outputs. Deletion of rpaA abrogates gene expression rhythms globally and arrests cells in a dawn-like expression state.

Two antagonistic clock-regulated histidine kinases time the activation of circadian gene expression.

The cyanobacterial circadian pacemaker consists of a three-protein clock--KaiA, KaiB, and KaiC--that generates oscillations in the phosphorylation state of KaiC. Here we investigate how temporal information encoded in KaiC phosphorylation is transduced to RpaA, a transcription factor required for circadian gene expression. We show that phosphorylation of RpaA is regulated by two antagonistic histidine kinases, SasA and CikA, which are sequentially activated at distinct times by the Kai clock complex.

Tunable signal processing through modular control of transcription factor translocation.

Signaling pathways can induce different dynamics of transcription factor (TF) activation. We explored how TFs process signaling inputs to generate diverse dynamic responses. The budding yeast general stress-responsive TF Msn2 acted as a tunable signal processor that could track, filter, or integrate signals in an input-dependent manner.

Hog1 controls global reallocation of RNA Pol II upon osmotic shock in Saccharomyces cerevisiae.

When challenged with osmotic shock, Saccharomyces cerevisiae induces hundreds of genes, despite a concurrent reduction in overall transcriptional capacity. The stress-responsive MAP kinase Hog1 activates expression of specific genes through interactions with chromatin remodeling enzymes, transcription factors, and RNA polymerase II. However, it is not clear whether Hog1 is involved more globally in modulating the cell's transcriptional program during stress, in addition to activating specific genes.

Integrated approaches reveal determinants of genome-wide binding and function of the transcription factor Pho4.

DNA sequences with high affinity for transcription factors occur more frequently in the genome than instances of genes bound or regulated by these factors. It is not clear what factors determine the genome-wide pattern of binding or regulation for a given transcription factor. We used an integrated approach to study how trans influences shape the binding and regulatory landscape of Pho4, a budding yeast transcription factor activated in response to phosphate limitation.

Transcriptional regulatory circuits: predicting numbers from alphabets.

Transcriptional regulatory circuits govern how cis and trans factors transform signals into messenger RNA (mRNA) expression levels. With advances in quantitative and high-throughput technologies that allow measurement of gene expression state in different conditions, data that can be used to build and test models of transcriptional regulation is being generated at a rapid pace. Here, we review experimental and computational methods used to derive detailed quantitative circuit models on a small scale and cruder, genome-wide models on a large scale.

Structure and function of a transcriptional network activated by the MAPK Hog1.

Cells regulate gene expression using a complex network of signaling pathways, transcription factors and promoters. To gain insight into the structure and function of these networks, we analyzed gene expression in single- and multiple-mutant strains to build a quantitative model of the Hog1 MAPK-dependent osmotic stress response in budding yeast. Our model reveals that the Hog1 and general stress (Msn2/4) pathways interact, at both the signaling and promoter level, to integrate information and create a context-dependent response.