TCP Transcription factors at the interface between environmental challenges and the plant’s growth responses

Danisman S. TCP Transcription factors at the interface between environmental challenges and the plant’s growth responses. Frontiers of Plant Science. 2016;7: 1930.Plants are sessile and as such their reactions to environmental challenges differ from those of mobile organisms. Many adaptions involve growth responses and hence, growth regulation is one of the most crucial biological processes for plant survival and fitness. The plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PCF1 (TCP) transcription factor family is involved in plant development from cradle to grave, i.e., from seed germination throughout vegetative development until the formation of flowers and fruits. TCP transcription factors have an evolutionary conserved role as regulators in a variety of plant species, including orchids, tomatoes, peas, poplar, cotton, rice and the model plant Arabidopsis. Early TCP research focused on the regulatory functions of TCPs in the development of diverse organs via the cell cycle. Later research uncovered that TCP transcription factors are not static developmental regulators but crucial growth regulators that translate diverse endogenous and environmental signals into growth responses best fitted to ensure plant fitness and health. I will recapitulate the research on TCPs in this review focusing on two topics: the discovery of TCPs and the elucidation of their evolutionarily conserved roles across the plant kingdom, and the variety of signals, both endogenous (circadian clock, plant hormones) and environmental (pathogens, light, nutrients), TCPs respond to in the course of their developmental roles

a simple tool for the analysis of periodic cotyledon and leaf movement in Arabidopsis thaliana

Background The analysis of circadian leaf movement rhythms is a simple yet effective method to study effects of treatments or gene mutations on the circadian clock of plants. Currently, leaf movements are analysed using time lapse photography and subsequent bioinformatics analyses of leaf movements. Programs that are used for this purpose either are able to perform one function (i.e. leaf tip detection or rhythm analysis) or their function is limited to specific computational environments. We developed a leaf movement analysis tool—PALMA—that works in command line and combines image extraction with rhythm analysis using Fast Fourier transformation and non-linear least squares fitting. Results We validated PALMA in both simulated time series and in experiments using the known short period mutant sensitivity to red light reduced 1 (srr1-1). We compared PALMA with two established leaf movement analysis tools and found it to perform equally well. Finally, we tested the effect of reduced iron conditions on the leaf movement rhythms of wild type plants. Here, we found that PALMA successfully detected period lengthening under reduced iron conditions. Conclusions PALMA correctly estimated the period of both simulated and real-life leaf movement experiments. As a platform-independent console-program that unites both functions needed for the analysis of circadian leaf movements it is a valid alternative to existing leaf movement analysis tools

Computational exploration of cis-regulatory modules in rhythmic expression data using the “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG) programs

Bekiaris PS, Tekath T, Staiger D, Danisman S. Computational exploration of cis-regulatory modules in rhythmic expression data using the “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG) programs. PLOS ONE. 2018;13(1): e0190421.Understanding the effect of cis-regulatory elements (CRE) and clusters of CREs, which are called cis-regulatory modules (CRM), in eukaryotic gene expression is a challenge of computational biology. We developed two programs that allow simple, fast and reliable analysis of candidate CREs and CRMs that may affect specific gene expression and that determine positional features between individual CREs within a CRM. The first program, “Exploration of Distinctive CREs and CRMs” (EDCC), correlates candidate CREs and CRMs with specific gene expression patterns. For pairs of CREs, EDCC also determines positional preferences of the single CREs in relation to each other and to the transcriptional start site. The second program, “CRM Network Generator” (CNG), prioritizes these positional preferences using a neural network and thus allows unbiased rating of the positional preferences that were determined by EDCC. We tested these programs with data from a microarray study of circadian gene expression in Arabidopsis thaliana. Analyzing more than 1.5 million pairwise CRE combinations, we found 22 candidate combinations, of which several contained known clock promoter elements together with elements that had not been identified as relevant to circadian gene expression before. CNG analysis further identified positional preferences of these CRE pairs, hinting at positional information that may be relevant for circadian gene expression. Future wet lab experiments will have to determine which of these combinations confer daytime specific circadian gene expression

The plant leaf movement analyzer (PALMA): a simple tool for the analysis of periodic cotyledon and leaf movement in Arabidopsis thaliana

Wagner L, Schmal C, Staiger D, Danisman S. The plant leaf movement analyzer (PALMA): a simple tool for the analysis of periodic cotyledon and leaf movement in Arabidopsis thaliana. Plant Methods. 2017;13(1): 2.Background The analysis of circadian leaf movement rhythms is a simple yet effective method to study effects of treatments or gene mutations on the circadian clock of plants. Currently, leaf movements are analysed using time lapse photography and subsequent bioinformatics analyses of leaf movements. Programs that are used for this purpose either are able to perform one function (i.e. leaf tip detection or rhythm analysis) or their function is limited to specific computational environments. We developed a leaf movement analysis tool—PALMA—that works in command line and combines image extraction with rhythm analysis using Fast Fourier transformation and non-linear least squares fitting. Results We validated PALMA in both simulated time series and in experiments using the known short period mutant sensitivity to red light reduced 1 (srr1-1). We compared PALMA with two established leaf movement analysis tools and found it to perform equally well. Finally, we tested the effect of reduced iron conditions on the leaf movement rhythms of wild type plants. Here, we found that PALMA successfully detected period lengthening under reduced iron conditions. Conclusions PALMA correctly estimated the period of both simulated and real-life leaf movement experiments. As a platform-independent console-program that unites both functions needed for the analysis of circadian leaf movements it is a valid alternative to existing leaf movement analysis tools

Differential control of pre-invasive and post-invasive antibacterial defense by the Arabidopsis circadian clock

Korneli C, Danisman S, Staiger D. Differential control of pre-invasive and post-invasive antibacterial defense by the Arabidopsis circadian clock. Plant & Cell Physiology. 2014;55(9):1613-1622.Plants show a suite of inducible defense responses against bacterial pathogens. Here we investigate in detail the effect of the circadian clock on these reactions in Arabidopsis thaliana. The magnitude of immune responses elicited by flg22, by virulent and by avirulent Pseudomonas syringae strains depends on the time of day of inoculation. The oxidative burst is stronger when flg22 is infiltrated in the morning in wild-type plants but not in the arrhythmic clock mutant lux arrhythmo/phytoclock1 (pcl1), and thus is controlled by the endogenous clock. Similarly, when bacteria are syringe-infiltrated into the leaf, defense gene induction is higher and bacterial growth is suppressed more strongly after morning inoculation in wild-type but not in pcl1 plants. Furthermore, cell death associated with the hypersensitive response was found to be under clock control. Notably, the clock effect depends on the mode of infection: upon spray inoculation onto the leaf surface, defense gene induction is higher and bacterial growth is suppressed more strongly upon evening inoculation. This different phasing of pre-invasive and post-invasive defense relates to clock-regulated stomatal movement. In particular, TIME FOR COFFEE may impact pathogen defense via clock-regulated stomata movement apart from its known role in time-of-day-dependent jasmonate responses. Taken together, these data highlight the importance of the circadian clock for the control of different immune responses at distinct times of the day. The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: [email protected]

Time to Network: The Molecular Blueprint of the Circadian Timing System in Plants

Danisman S, Mateos JL, Staiger D. Time to Network: The Molecular Blueprint of the Circadian Timing System in Plants. In: Mancuso S, Shabala S, eds. Rhythms in Plants. Cham: Springer International Publishing; 2015: 257-278

Representative output of the CNG analysis.

<p>A) Distribution of p-values for binomial order test. B) Distribution of p-values for distance G-test. C) Distribution of Bowley skewness analysis.</p

MOESM2 of The plant leaf movement analyzer (PALMA): a simple tool for the analysis of periodic cotyledon and leaf movement in Arabidopsis thaliana

Additional file 2. Programme files

Positions of ACANTACN and G box motifs in photosystem subunit gene promoters and correlation with circadian gene expression.

<p>A) Positions of ACANTACN (white arrows) and the G box MCACGTGGC (black arrows) CREs in promoters of photosystem subunit genes. Blue arrows indicate CDS in 5’-3’ direction (introns are ignored), thicker blue lines indicate 5’ and 3’ UTRs. Thin blue line represents 1000 bp upstream region of the TSS. B) Circadian gene expression of the same photosystem genes as given by DIURNAL [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190421#pone.0190421.ref081" target="_blank">81</a>].</p