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A subset of group S1 bZIP transcription factors controls resource management during starvation and recovery in Arabidopsis

ABSTRACT: A subset of group S1 bZIP transcription factors controls resource management during starvation and recovery in Arabidopsis

PROVIDER: PRJNA1284228 | ENA |

REPOSITORIES: ENA

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A subset of group S1 bZIP transcription factors controls resource management during starvation and recovery in Arabidopsis

Project description:To unravel the individual functions of group S1 bZIP transcription factors during dark induced senescence, we made use of Arabidopsis wildtype (WT) as well as single (bzip1 and bzip53) and higher-order S1 bzip mutants (bzip1/53, bzip2/11/44, bzip1/2/11/44/53) and performed RNAseq analysis during the day (Zeitgeber time 6) and extended night conditions (6h, 30h and 78h).

2025-06-30 | GSE301177 | GEO

A distinct subset of the Arabidopsis group S1 basic leucine zipper transcription factors controls plant resource management during starvation and recovery

Project description:Plants possess an enormous plasticity to adapt their metabolism to the fluctuating energy supply in a natural environment. Using dark-induced senescence (DIS) as an experimental system, a mutant study combining phenotypical, transcriptomic and Chromatin Immunoprecipitation Sequencing (ChIPseq) approaches identifies distinct members of the Arabidopsis group S1 basic leucine zipper transcription factors that orchestrate the starvation response. While excluding bZIP2, bZIP11 and bZIP44 to function in DIS, the in part redundantly acting bZIP1 and bZIP53 control a co-expression network governing amino acid catabolism and transport, gluconeogenesis and energy homeostasis. Moreover, they regulate genes involved in asparagine – glutamine balance, which are critical for C/N homeostasis. This transcriptional reprogramming in resource management is required for survival during starvation and regaining meristematic activity during recovery from stress. Thus, we provide insights into the transcriptional control of plant resource and energy management during starvation. Finally, this work sheds light on the discrepancy between in vitro DNA-binding and overexpression studies versus mutant analyses and in vivo DNA-binding, providing a critical view on how to define specific transcription factor functions within large families.

2025-07-03 | GSE286485 | GEO

In vitro, genomic context identification of transcription factor binding sites for bZIP C/S1 homodimers and heterodimers

Project description:In eukaryotes, many transcription factors (TF) usually form dimers or oligomers with itself or other TFs to regulate gene expression. To study how homo- and heterodimerization of TFs affect DNA binding specificity, we developed a double DNA Affinity Purification sequencing (double DAP-seq; dDAP-seq) technique that maps heterodimer binding sites in endogenous genome context and applied it to elucidate the binding profiles of homo- and heterodimers of the Group C and S1 basic leucine zipper (bZIP) transcription factors in Arabidopsis. Genome-wide binding profiles of twenty pairs of bZIP C/S1 heterodimers and bZIP S1 homodimers revealed that heterodimerization significantly expands the DNA binding preferences of homodimers, creating unique binding sites and target gene functions. In addition to the classical ACGT elements recognized by plant bZIPs, we found the Group C/S1 dimers bind to sequence motifs that might share an origin with the yeast bZIP GCN4. Further analysis of heterodimer-specific binding sequences uncovered two types of motif recognition patterns that mediate heterodimer specificity. Our study shed light on the functions and mechanisms of TF dimerization and demonstrated the potential of dDAP-seq in deciphering the complexity of these interactions within or across TF families.

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A distinct subset of the Arabidopsis group S1 basic leucine zipper transcription factors controls plant resource management during starvation and recovery

Project description:A distinct subset of the Arabidopsis group S1 basic leucine zipper transcription factors controls plant resource management during starvation and recovery

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Crosstalk between two bZIP signaling pathways orchestrates salt-induced metabolic reprogramming in Arabidopsis roots

Project description:Soil salinity increasingly causes crop losses worldwide. Although roots are the primary targets of salt stress, the signaling networks that facilitate metabolic reprogramming to induce stress tolerance are less understood than those in leaves. Here, a combination of transcriptomic and metabolic approaches was performed in salt-treated Arabidopsis thaliana roots, which revealed that the group S1 basic leucine zipper transcription factors bZIP1 and bZIP53 reprogram primary C- and N-metabolism. In particular, gluconeogenesis and amino acid catabolism are affected by these transcription factors. Importantly, bZIP1 expression reflects cellular stress and energy status in roots. In addition to the well-described abiotic stress response pathway initiated by the hormone abscisic acid (ABA) and executed by SnRK2 (Snf1-RELATED-PROTEIN-KINASE2) and AREB-like bZIP factors, we identify a structurally related ABA-independent signaling module consisting of SnRK1s and S1 bZIPs. Crosstalk between these signaling pathways recruits particular bZIP factor combinations to establish at least four distinct gene expression patterns. Understanding this signaling network provides a framework for securing future crop productivity.

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S1 basic leucine zipper transcription factors shape plant architecture by controlling C/N partitioning to apical and lateral organs

Project description:To decipher gene expression controlled by the five highly homologous group S1 bZIP transcription factors during the reproductive growth phase of Arabidopsis thaliana, we generated triple (bzip2/-11/-44) and quintuple (bzip1/-2/-11/-44/-53) mutants of these factors using CRISPR/Cas9 and analysed gene expression in distinct C source (source leaves) or C sink (sink leaves, rosette buds, flowers) tissues.

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Crosstalk between two bZIP signaling pathways orchestrates salt-induced metabolic reprogramming in Arabidopsis roots

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Project description:S1 Metagenome

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In vitro, genomic context identification of transcription factor binding sites for bZIP C/S1 homodimers and heterodimers

Project description:In vitro, genomic context identification of transcription factor binding sites for bZIP C/S1 homodimers and heterodimers

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