Background Transcription factors of the basic leucine zipper (bZIP) family control important processes in all eukaryotes. In plants, bZIPs are regulators of many central developmental and physiological processes including photomorphogenesis, leaf and seed formation, energy homeostasis, and abiotic and biotic stress responses. Here we performed a comprehensive phylogenetic analysis of bZIP genes from algae, mosses, ferns, gymnosperms and angiosperms. Methodology/Principal Findings We identified 13 groups of bZIP homologues in angiosperms, three more than known before, that represent 34 Possible Groups of Orthologues (PoGOs). The 34 PoGOs may correspond to the complete set of ancestral angiosperm bZIP genes that participated in the diversification of flowering plants. Homologous genes dedicated to seed-related processes and ABA-mediated stress responses originated in the common ancestor of seed plants, and three groups of homologues emerged in the angiosperm lineage, of which one group plays a role in optimizing the use of energy. Conclusions/Significance Our data suggest that the ancestor of green plants possessed four bZIP genes functionally involved in oxidative stress and unfolded protein responses that are bZIP-mediated processes in all eukaryotes, but also in light-dependent regulations. The four founder genes amplified and diverged significantly, generating traits that benefited the colonization of new environments.

https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0002944&type=printable

The role of bZIP transcription factors in green plant evolution: adaptive features emerging from four founder genes.

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. This study lays out a path to identifying and characterizing the role of signal integration and processing in other gene regulatory networks.

/pdf/structure-and-function-of-a-transcriptional-network-4yftzzsa6r.pdf

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

DNA damage-induced reactive oxygen species (ROS) stress response in Saccharomyces cerevisiae.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2005.12.050

Yeast ABC transporters – A tale of sex, stress, drugs and aging

Characterization of the calcium-mediated response to alkaline stress in Saccharomyces cerevisiae.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1016/j.febslet.2004.03.119

Yeast activator proteins and stress response: an overview ☆

YAP4, a member of the yeast activator protein (YAP )g ene family, is induced in response to osmotic shock in the yeast Saccharomyces cerevisiae. The null mutant displays mild and moderate growth sensitivity at 0.4 M and 0.8 M NaCl respectively, a fact that led us to analyse YAP4 mRNA levels in the hog1 (high osmolarity glycerol) mutant. The data obtained show a complete abolition of YAP4 gene expression in this mutant, placing YAP4 under the HOG response pathway. YAP4 overexpressionnotonlysuppressestheosmosensitivityphenotype of the yap4 mutant but also relieves that of the hog1 mutant. Induction,undertheconditionstestedsofar,requiresthepresence of the transcription factor Msn2p, but not of Msn4p, as YAP4 mRNA levels are depleted by at least 75% in the msn2 mutant. This result was further substantiated by the fact that full YAP4 induction requires the two more proximal stress response elements. Furthermore we find that GCY1, encoding a putativeglyceroldehydrogenase,GPP2,encodingaNAD-dependent glycerol-3-phosphate phosphatase, and DCS2, a homologue to a decapping enzyme, have decreased mRNA levels in the yap4deleted strain. Our data point to a possible, as yet not entirely understood, role of the YAP4 in osmotic stress response.

/pdf/expression-of-yap4-in-saccharomyces-cerevisiae-under-osmotic-5gtj8w5z36.pdf

Expression of YAP4 in Saccharomyces cerevisiae under osmotic stress.

Exposure of Saccharomyces cerevisiae to several environmental insults, including conditions of oxidative, heavy metal, metalloid and heat stress, induces the expression of the YAP4 gene, previously shown to play a role in the response to hyperosmotic stress. Expression analyses in several mutant strains under pro-oxidant conditions have determined that YAP4 is regulated by the transactivators Yap1p and Msn2p. Mutation of either the Yap1p-response element (YRE), located at − 517 bp from the ATG, or the most proximal stress response element (STRE) at −430 bp, is shown to strongly compromise YAP4 gene expression under these conditions. Furthermore, these two mutations in combination lead to a severe depletion of detectable mRNA levels, indicating interplay between the transcription factors Yap1p and Msn2p in the regulation of YAP4 transcription. Transcriptional activation of this gene reflects a concomitant increase in Yap4p protein levels that appear phosphorylated upon stress and negatively regulated by protein kinase A. Yap4p amino acid residues Ser89, Ser196 and Thr241 are shown to be required for protein phosphorylation and/or protein stability. Copyright © 2004 John Wiley & Sons, Ltd.

YAP4 gene expression is induced in response to several forms of stress in Saccharomyces cerevisiae

The budding yeast Saccharomyces cerevisiae possesses a very flexible and complex programme of gene expression when exposed to a plethora of environmental insults. Therefore, yeast cell homeostasis control is achieved through a highly coordinated mechanism of transcription regulation involving several factors, each performing specific functions. Here, we present our current knowledge of the function of the yeast activator protein family, formed by eight basic-leucine zipper trans-activators, which have been shown to play an important role in stress response.

https://febs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1742-4658.2005.04695.x

The yeast stress response. Role of the Yap family of b-ZIP transcription factors. The PABMB Lecture delivered on 30 June 2004 at the 29th FEBS Congress in Warsaw.

The capacity for adaptation to changes in intra- andextracellular conditions is a universal prerequisite foran organism’s survival and evolution. The existence ofmolecular mechanisms of response, repair and adapta-tion, many of which are greatly conserved across nat-ure, endows the cell with the plasticity it requires toadjust to its ever-changing environment, a homeostaticevent that is termed the stress response. Through thesensing and transduction of the stress signal into thenucleus, a genetic reprogramming occurs that leads, onthe one hand, to a decrease in the expression of house-keeping genes and protein synthesis and, on the otherhand, to an enhancement of the expression of genesencoding stress proteins. These include molecularchaperones responsible for maintaining protein folding,transcription factors that further modulate geneexpression and a diverse network of players includingmembrane transporters and proteins involved in repairand detoxiﬁcation pathways, nutrient metabolism, andosmolyte production, to name a few. Survival andgrowth resumption imply successful cellular adaptationto the new conditions as well as the repair of damageincurred to the cell. Although speciﬁc stress conditionselicit distinct cellular responses, underlying gene

Tracy Nevitt

Papers

Yeast activator proteins and stress response: an overview ☆

Expression of YAP4 in Saccharomyces cerevisiae under osmotic stress.

YAP4 gene expression is induced in response to several forms of stress in Saccharomyces cerevisiae

The yeast stress response. Role of the Yap family of b-ZIP transcription factors. The PABMB Lecture delivered on 30 June 2004 at the 29th FEBS Congress in Warsaw.

Role of the Yap family of b-ZIP transcription factors The PABMB Lecture delivered on 30 June 2004 at the 29th FEBS Congress in Warsaw