scholarly journals Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway

2017 ◽  
Author(s):  
Bin Z. He ◽  
Xu Zhou ◽  
Erin K. O’Shea
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Physiological Response ◽  
Phosphate Starvation ◽  
Closely Related Species ◽  
Starvation Response ◽  
Evolutionary Mechanism ◽  
Functional Roles ◽  
Phosphate Response ◽  
Starvation Conditions

AbstractIn S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. Our work reveals an evolutionary mechanism for rapidly expanding the targets of a transcription factor by changing its dependence on a co-activator, potentially refining the physiological response it regulates.

scholarly journals Defining the DNA Binding Site Recognized by the Fission Yeast Zn 2 Cys 6 Transcription Factor Pho7 and Its Role in Phosphate Homeostasis

mBio ◽  
2017 ◽  
Vol 8 (4) ◽  
Author(s):  
Beate Schwer ◽  
Ana M. Sanchez ◽  
Angad Garg ◽  
Debashree Chatterjee ◽  
Stewart Shuman
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Fission Yeast ◽  
Phosphate Starvation ◽  
Phosphate Homeostasis ◽  
Starvation Response ◽  
Recognition Sites ◽  
Transcription Regulators

ABSTRACT Fission yeast phosphate homeostasis entails transcriptional induction of genes encoding phosphate-mobilizing proteins under conditions of phosphate starvation. Transcription factor Pho7, a member of the Zn 2 Cys 6 family of fungal transcription regulators, is the central player in the starvation response. The DNA binding sites in the promoters of phosphate-responsive genes have not been defined, nor have any structure-function relationships been established for the Pho7 protein. Here we narrow this knowledge gap by (i) delineating an autonomous DNA-binding domain (DBD) within Pho7 that includes the Zn 2 Cys 6 module, (ii) deploying recombinant Pho7 DBD in DNase I footprinting and electrophoretic mobility shift assays (EMSAs) to map the Pho7 recognition sites in the promoters of the phosphate-regulated pho1 and tgp1 genes to a 12-nucleotide sequence motif [5′-TCG(G/C)(A/T)xxTTxAA], (iii) independently identifying the same motif as a Pho7 recognition element via in silico analysis of available genome-wide ChIP-seq data, (iv) affirming that mutations in the two Pho7 recognition sites in the pho1 promoter efface pho1 expression in vivo , and (v) establishing that the zinc-binding cysteines and a pair of conserved arginines in the DBD are essential for Pho7 activity in vivo . IMPORTANCE Fungi respond to phosphate starvation by inducing the transcription of a set of phosphate acquisition genes that comprise a phosphate regulon. Pho7, a member of the Zn 2 Cys 6 family of fungal transcription regulators, is the central player in the phosphate starvation response in fission yeast. The present study identifies a 12-nucleotide Pho7 DNA binding motif [5′-TCG(G/C)(A/T)xxTTxAA] in the promoters of phosphate-regulated genes, pinpoints DNA and protein features important for Pho7 binding to DNA, and correlates them with Pho7-dependent gene expression in vivo . The results highlight distinctive properties of Pho7 vis-a-vis other fungal zinc binuclear cluster transcription factors as well as the divergent cast of transcription factors deployed for phosphate homeostasis in fission yeast versus budding yeast.

scholarly journals Genome wide identification of NAC transcription factors and their role in abiotic stress tolerance in Chenopodium quinoa

2019 ◽  
Author(s):  
Nouf Owdah Alshareef ◽  
Elodie Rey ◽  
Holly Khoury ◽  
Mark Tester ◽  
Sandra M. Schmöckel
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Abiotic Stress ◽  
Stress Tolerance ◽  
Abiotic Stresses ◽  
Abiotic Stress Tolerance ◽  
Chenopodium Quinoa ◽  
Phosphate Starvation ◽  
Water Deficiency ◽  
Genome Wide

AbstractChenopodium quinoa Willd. (quinoa) is a pseudocereal with high nutritional value and relatively high tolerance to several abiotic stresses, including water deficiency and salt stress, making it a suitable plant for the study of mechanisms of abiotic stress tolerance. NAC (NAM, ATAF and CUC) transcription factors are involved in a range of plant developmental processes and in the response of plants to biotic and abiotic stresses. In the present study, we perform a genome-wide comprehensive analysis of the NAC transcription factor gene family in quinoa. In total, we identified 107 quinoa NAC transcription factor genes, distributed equally between sub-genomes A and B. They are phylogenetically clustered into two major groups and 18 subgroups. Almost 75% of the identified CqNAC genes were duplicated two to seven times and the remaining 25% of the CqNAC genes were found as a single copy. We analysed the transcriptional responses of the identified quinoa NAC TF genes in response to various abiotic stresses. The transcriptomic data revealed 28 stress responsive CqNAC genes, where their expression significantly changed in response to one or more abiotic stresses, including salt, water deficiency, heat and phosphate starvation. Among these stress responsive NACs, some were previously known to be stress responsive in other species, indicating their potentially conserved function in response to abiotic stress across plant species. Six genes were differentially expressed specifically in response to phosphate starvation but not to other stresses, and these genes may play a role in controlling plant responses to phosphate deficiency. These results provide insights into quinoa NACs that could be used in the future for genetic engineering or molecular breeding.

scholarly journals Effect of heat and drought stress on the expression of regulatory transcription factors and the genes involved in different metabolic pathways

2018 ◽  
Vol 7 (1) ◽  
pp. 1941 ◽  
Author(s):  
Murali O. ◽  
Santosh Kumar Mehar
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Drought Stress ◽  
Metabolic Pathways ◽  
Stress Factors ◽  
Cell Organelles ◽  
Functional Roles ◽  
Regulatory Processes ◽  
Efficient Management ◽  
Expression Of Genes

Plants never encounter stress factors, whether biotic or abiotic in sequence. Mostly they have to face multiple environmental factors in suboptimal level (stressful) at the same time. As a result, the strategy of the plant to survive in such situations demands handling of multiple stresses at the same time by efficient management of the genetic repertoire that the plant has. The plant achieves this by altering expression of transcription factors that regulate the activity of different genes, whose products themselves play the structural and functional roles. In the present study, differentially regulated genes under heat and drought stress from different microarray studies were analyzed to assess the kind of metabolic pathways that are specifically altered (promoted or sacrificed) under heat and drought stress and the transcription factor families which have the governing role in such regulatory processes. It was observed that expression of genes related to metabolism, specifically in the cell organelles like plastids and mitochondria is differentially regulated. Some transcription factor families like AP2-EREBP, NAC, C2H2 and MYB play more important role in the two kinds of stress conditions.

scholarly journals Under phosphate starvation conditions, Fe and Al trigger accumulation of the transcription factor STOP1 in the nucleus of Arabidopsis root cells

2019 ◽  
Vol 99 (5) ◽  
pp. 937-949 ◽  
Author(s):  
Christian Godon ◽  
Caroline Mercier ◽  
Xiaoyue Wang ◽  
Pascale David ◽  
Pierre Richaud ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Phosphate Starvation ◽  
Root Cells ◽  
Arabidopsis Root ◽  
Starvation Conditions

scholarly journals Rice SPX6 negatively regulates the phosphate starvation response through suppression of the transcription factor PHR2

2018 ◽  
Vol 219 (1) ◽  
pp. 135-148 ◽  
Author(s):  
Yongjia Zhong ◽  
Yuguang Wang ◽  
Jiangfan Guo ◽  
Xinlu Zhu ◽  
Jing Shi ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Phosphate Starvation ◽  
Starvation Response ◽  
Phosphate Starvation Response

scholarly journals OsARF16, a transcription factor, is required for auxin and phosphate starvation response in rice (Oryza sativaL.)

2012 ◽  
Vol 36 (3) ◽  
pp. 607-620 ◽  
Author(s):  
CHENJIA SHEN ◽  
SUIKANG WANG ◽  
SAINA ZHANG ◽  
YANXIA XU ◽  
QIAN QIAN ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Phosphate Starvation ◽  
Starvation Response ◽  
Phosphate Starvation Response

scholarly journals Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Bin Z He ◽  
Xu Zhou ◽  
Erin K O’Shea
Keyword(s):  
Gene Regulatory Networks ◽  
Regulatory Networks ◽  
Phosphate Starvation ◽  
Structure And Function ◽  
Rapid Expansion ◽  
Closely Related Species ◽  
Starvation Response ◽  
Combinatorial Regulation ◽  
Gene Regulatory ◽  
And Function

Although combinatorial regulation is a common feature in gene regulatory networks, how it evolves and affects network structure and function is not well understood. In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are required for gene induction and survival during phosphate starvation. In the related human commensal C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate starvation and is only partially required for inducing PHO genes. Phylogenetic survey suggests that reduced dependence on Pho2 evolved in C. glabrata and closely related species. In S. cerevisiae, less Pho2-dependent Pho4 orthologs induce more genes. In C. glabrata, its Pho4 binds to more locations and induces three times as many genes as Pho4 in S. cerevisiae does. Our work shows how evolution of combinatorial regulation allows for rapid expansion of a gene regulatory network’s targets, possibly extending its physiological functions.

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