Illuminating light, cytokinin, and ethylene signalling crosstalk in plant development: Fig. 1.

Žďárská, Markéta; Dobisová, Tereza; Gelová, Zuzana; Pernisová, Markéta; Dabravolski, Siarhei A.; Hejátko, Jan

doi:10.1093/jxb/erv261

Cited by 79 publications

(61 citation statements)

References 241 publications

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“…S4, B and C). Taken together, the molecular nature of HY1, together with the previously reported interaction of light and cytokinin signaling pathways [reviewed by Zdarska et al (2015)], led us to study the role of light in the control of CKI1 expression.…”

Section: Light Regulates Expression Of Cki1mentioning

confidence: 99%

Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1

et al. 2017

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(J.H.).In plants, the multistep phosphorelay (MSP) pathway mediates a range of regulatory processes, including those activated by cytokinins. The cross talk between cytokinin response and light has been known for a long time. However, the molecular mechanism underlying the interaction between light and cytokinin signaling remains elusive. In the screen for upstream regulators we identified a LONG PALE HYPOCOTYL (LPH) gene whose activity is indispensable for spatiotemporally correct expression of CYTOKININ INDEPENDENT1 (CKI1), encoding the constitutively active sensor His kinase that activates MSP signaling. lph is a new allele of HEME OXYGENASE1 (HY1) that encodes the key protein in the biosynthesis of phytochromobilin, a cofactor of photoconvertible phytochromes. Our analysis confirmed the light-dependent regulation of the CKI1 expression pattern. We show that CKI1 expression is under the control of phytochrome A (phyA), functioning as a dual (both positive and negative) regulator of CKI1 expression, presumably via the phyA-regulated transcription factors (TF) PHYTOCHROME INTERACTING FACTOR3 and CIRCADIAN CLOCK ASSOCIATED1. Changes in CKI1 expression observed in lph/hy1-7 and phy mutants correlate with misregulation of MSP signaling, changed cytokinin sensitivity, and developmental aberrations that were previously shown to be associated with cytokinin and/or CKI1 action. Besides that, we demonstrate a novel role of phyA-dependent CKI1 expression in the hypocotyl elongation and hook development during skotomorphogenesis. Based on these results, we propose that the light-dependent regulation of CKI1 provides a plausible mechanistic link underlying the well-known interaction between light-and cytokinin-controlled plant development.

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Section: Light Regulates Expression Of Cki1mentioning

confidence: 99%

Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1

et al. 2017

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“…In addition, we saw clear associations between ETR1 and AHK3 in individual PLC subgraphs. Such association highlights crosstalk already known between CK and ethylene signaling pathways 22 . The co-occurrence pathway was relatively sparse in contrast to the metabolic pathways (Supplementary Figure 5 online).…”

Section: Discussionmentioning

confidence: 71%

“…CK pathway includes both transcription activating and repressing activities (via response regulators) and post-transcriptional (phosphorylations) and would therefore be an excellent test of PLC applicability on associations expected to be more complex than in metabolic pathways. In addition, we included other histidine kinases integrating other signals and known to crosstalk with the CK pathway 22 . We therefore included 2 ethylene receptors, ETR1 and ERS1 to determine whether they could be clustered with CK histidine kinase.…”

Section: Resultsmentioning

confidence: 99%

Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks

Liesecke

Daudu

Bernonville

et al. 2018

Preprint

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10Co-expression networks are essential tools to infer biological associations between gene products and predict gene annotation. Global networks can be analyzed at the transcriptome wide scale or after querying them with a set of guide genes to capture the transcriptional landscape of a given pathway in a process named Pathway Level Correlation (PLC). A critical step in network construction remains the definition of gene co-expression. In the present work, we compared how Pearson Correlation Coefficient (PCC), Spearman Correlation Coefficient (SCC), their respective ranked values (Highest Reciprocal Rank (HRR)), Mutual Information (MI) and Partial Correlations (PC) performed on global networks and PLCs. This evaluation was conducted on the model plant Arabidopsis thaliana using microarray and differently pre-processed RNA-seq datasets. We particularly evaluated how dataset x distance measurement combinations performed in 5 PLCs corresponding to 4 well described plant metabolic pathways (phenylpropanoid, carbohydrate, fatty acid and terpene metabolisms) and the cytokinin signaling pathway. Our present work highlights how PCC ranked with HRR is better suited for global network construction and PLC with microarray and RNA-seq data than other distance methods, especially to cluster genes in partitions similar to biological subpathways. 11 Introduction 12Constructing global gene co-expression networks is a popular approach to highlight transcriptional relationships (edges) 13 between genes (vertices). The 'Guilt-by-Association' (GBA) principle supposes that genes sharing similar functions are 14 preferentially connected and aims at predicting new functions for proteins by determining how their respective encoding 15 genes are co-expressed with others using a reference dataset containing known gene functions such as the Gene Ontology 16 (GO) 1 . Defining edges connecting genes remains a critical step in global co-expression network construction. Expression 17 data (microarray or RNA-seq) are used to construct expression matrices (genes x samples) and to calculate a distance or 18 a similarity for each possible gene pair. The resulting pairwise distance matrix is then thresholded to obtain an adjacency 19 matrix that discriminates relevant edges. Only edges with a distance below (or a similarity above) the set threshold are 20 considered significant and retained for network construction. The procedure is expected to remove non biologically relevant 21 gene associations while retaining the relevant ones and can be assessed with any reference dataset. Alternatively, guide gene sets 22 may be used to extract more human-readable information from large networks in a process named Pathway-Level Correlation 23 (PLC) 2-6 . This approach aims at capturing the best transcriptional associations of a gene set and at highlighting functional gene 24 groups such as known subpathways in this set. There are two types of approaches to determine transcriptional associations 25 of genes: those that are supervised and those that are unsu...

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“…Some other topics are also of interest but are somehow related to this or are less represented in the most recent literature. This is the case of plant developmental processes, plant-pathogen interactions, and responses to other biotic stresses [101][102][103][104].…”

Section: From Proteomics To Biologymentioning

confidence: 99%

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

et al. 2016

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The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.

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Illuminating light, cytokinin, and ethylene signalling crosstalk in plant development: Fig. 1.

Cited by 79 publications

References 241 publications

Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1

Light Controls Cytokinin Signaling via Transcriptional Regulation of Constitutively Active Sensor Histidine Kinase CKI1

Ranking genome-wide correlation measurements improves microarray and RNA-seq based global and targeted co-expression networks

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

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