Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays

BACKGROUND Organisms are able to anticipate changes in the daily environment with an internal oscillator know as the circadian clock. Transcription is an important mechanism in maintaining these oscillations. Here we explore, using whole genome tiling arrays, the extent of rhythmic expression patterns genome-wide, with an unbiased analysis of coding and noncoding regions of the Arabidopsis genome. RESULTS As in previous studies, we detected a circadian rhythm for approximately 25% of the protein coding genes in the genome. With an unbiased interrogation of the genome, extensive rhythmic introns were detected predominantly in phase with adjacent rhythmic exons, creating a transcript that, if translated, would be expected to produce a truncated protein. In some cases, such as the MYB transcription factor AT2G20400, an intron was found to exhibit a circadian rhythm while the remainder of the transcript was otherwise arrhythmic. In addition to several known noncoding transcripts, including microRNA, trans-acting short interfering RNA, and small nucleolar RNA, greater than one thousand intergenic regions were detected as circadian clock regulated, many of which have no predicted function, either coding or noncoding. Nearly 7% of the protein coding genes produced rhythmic antisense transcripts, often for genes whose sense strand was not similarly rhythmic. CONCLUSIONS This study revealed widespread circadian clock regulation of the Arabidopsis genome extending well beyond the protein coding transcripts measured to date. This suggests a greater level of structural and temporal dynamics than previously known

ParB deficiency in Pseudomonas aeruginosa destabilizes the partner protein ParA and affects a variety of physiological parameters

Deletions leading to complete or partial removal of ParB were introduced into the Pseudomonas aeruginosa chromosome. Fluorescence microscopy of fixed cells showed that ParB mutants lacking the C-terminal domain or HTH motif formed multiple, less intense foci scattered irregularly, in contrast to the one to four ParB foci per cell symmetrically distributed in wild-type P. aeruginosa. All parB mutations affected both bacterial growth and swarming and swimming motilities, and increased the production of anucleate cells. Similar effects were observed after inactivation of parA of P. aeruginosa. As complete loss of ParA destabilized its partner ParB it was unclear deficiency of which protein is responsible for the mutant phenotypes. Analysis of four parB mutants showed that complete loss of ParB destabilized ParA whereas three mutants that retained the N-terminal 90 aa of ParB did not. As all four parB mutants demonstrate the same defects it can be concluded that either ParB, or ParA and ParB in combination, plays an important role in nucleoid distribution, growth and motility in P. aeruginosa

Fluctuations in spo0A Transcription Control Rare Developmental Transitions in Bacillus subtilis

Phosphorylated Spo0A is a master regulator of stationary phase development in the model bacterium Bacillus subtilis, controlling the formation of spores, biofilms, and cells competent for transformation. We have monitored the rate of transcription of the spo0A gene during growth in sporulation medium using promoter fusions to firefly luciferase. This rate increases sharply during transient diauxie-like pauses in growth rate and then declines as growth resumes. In contrast, the rate of transcription of an rRNA gene decreases and increases in parallel with the growth rate, as expected for stable RNA synthesis. The growth pause-dependent bursts of spo0A transcription, which reflect the activity of the spo0A vegetative promoter, are largely independent of all known regulators of spo0A transcription. Evidence is offered in support of a “passive regulation” model in which RNA polymerase stops transcribing rRNA genes during growth pauses, thus becoming available for the transcription of spo0A. We show that the bursts are followed by the production of phosphorylated Spo0A, and we propose that they represent initial responses to stress that bring the average cell closer to the thresholds for transition to bimodally expressed developmental responses. Measurement of the numbers of cells expressing a competence marker before and after the bursts supports this hypothesis. In the absence of ppGpp, the increase in spo0A transcription that accompanies the entrance to stationary phase is delayed and sporulation is markedly diminished. In spite of this, our data contradicts the hypothesis that sporulation is initiated when a ppGpp-induced depression of the GTP pool relieves repression by CodY. We suggest that, while the programmed induction of sporulation that occurs in stationary phase is apparently provoked by increased flux through the phosphorelay, bet-hedging stochastic transitions to at least competence are induced by bursts in transcription

Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium

Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These “memory” effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to ‘remember’ 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy

Technical challenges in characterization of future CO2 storage site in a deep saline aquifer in the Paris basin. Lessons learned from practical application of site selection methodology

AbstractTo ensure safe behavior during the whole lifetime of the geological storage of CO2, site selection and its characterization are essential corner stones. This paper presents the different milestones and the results of each step of the site characterization implemented on a potential storage site in the Triassic deep saline aquifer of the Paris Basin. It addresses a well known theory and practical aspects and challenges of the first phase of real site identification carried out by Veolia Environnement and Geogreen.The initial static and dynamic characterization of the storage complex will mainly rely on available public or proprietary data. Different challenges related to the gathering and validation of existing data are discussed. The characterization methodology should aim at re-interpreting the available data in order to populate a dynamic model at semi-regional scale of the storage complex.2D Seismic data reprocessing made it possible to determine the local structure of the storage. Regional structural information must also been considered since industrial scale injection impacts a significant area with respect to overpressure extension. To complete the storage complex description, upper laying structures and aquifers must be adequately described up to the ground level. When elaborating such a 3D model, data consistency at the different scales should be carefully checked.Facies variations, porosity and both vertical and horizontal permeabilities will control storage capacity and well injectivity. Thus, an extensive log analysis is a major step in the characterization methodology. When available, core samples and flow tests must also be reconsidered to enhance the model quality. Furthermore, petrophysical interpretation of logs will improve site characterization and enable mineral trapping assessment. The consistent re-interpretation of available well logs will ensure proper site characterization in terms of reservoir and containment. Some examples are provided to illustrate the relevance of re-interpretation work.Building a 3-D geological model is a major integrating step of the available dataset on the area of interest both in terms of structure and heterogeneities at different scales (facies, mineral, petrophysical …). At this stage, the different assumptions should be carefully revisited in light of the available data. The geological uncertainties can then be estimated using a statistical approach, which highlights key petrophysical characteristics of the storage along with main risks that need to be assessed.The final step in the characterization methodology includes a dynamic assessment of the short term effects on injectivity and capacity, and of long term trapping mechanism. On the short term, potential interference with other sub-surface activities needs to be investigated along with the potential migration pathways (existing wells and faults). Models were elaborated at different scales. A near-wellbore model helped to estimate chemical induced effects. A storage site model helped to estimate overpressure and CO2 plume behaviors, and a model larger than the storage complex helped to identify migration pathways and constraint boundary conditions. Different assumptions and operational constraints were supposed to ensure the robustness of different injection scenarios. The results of corresponding dynamic simulations are presented and discussed