Class III Homeodomain-Leucine Zipper Gene Family Members Have Overlapping, Antagonistic, and Distinct Roles in Arabidopsis Development

Abscisic acid (ABA) plays a crucial role in various aspects of plant growth and development, including fruit development and ripening, seed dormancy, and involvement in response to various environmental stresses. In almost all higher plants, ABA signal transduction requires three core components; namely, PYR/PYL/RCAR ABA receptors (PYLs), type 2C protein phosphatases (PP2Cs), and class III SNF-1-related protein kinase 2 (SnRK2s). The exploration of these three core components is not comprehensive in soybean. This study identified the GmPYL-PP2C-SnRK2s gene family members by using the JGI Phytozome and NCBI database. The gene family composition, conservation, gene structure, evolutionary relationship, cis-acting elements of promoter regions, and its coding protein domains were analyzed. In the entire genome of the soybean, there are 21 PYLs, 36 PP2Cs, and 21 SnRK2s genes; further, by phylogenetic and conservation analysis, 21 PYLs genes are classified into 3 groups, 36 PP2Cs genes are classified into seven groups, and 21 SnRK2s genes are classified into 3 groups. The conserved motifs and domain analysis showed that all the GmPYLs gene family members contain START-like domains, the GmPP2Cs gene family contains PP2Cc domains, and the GmSnRK2s gene family contains S_TK domains, respectively. Furthermore, based on the high-throughput transcriptome sequencing data, the results showed differences in the expression patterns of GmPYL-PP2C-SnRK2s gene families in different tissue parts of the same variety, and the same tissue part of different varieties. Our study provides a basis for further elucidation of the identification of GmPYL-PP2C-SnRK2s gene family members and analysis of their evolution and expression patterns, which helps to understand the molecular mechanism of soybean response to abiotic stress. In addition, this provides a conceptual basis for future studies of the soybean ABA core signal pathway.

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Knockdown of OsHox33, a member of the class III homeodomain-leucine zipper gene family, accelerates leaf senescence in rice

Science China Life Sciences ◽

10.1007/s11427-013-4565-2 ◽

2013 ◽

Vol 56 (12) ◽

pp. 1113-1123 ◽

Cited By ~ 10

Author(s):

WeiJiang Luan ◽

Ao Shen ◽

ZhiPing Jin ◽

SuSheng Song ◽

ZhengLong Li ◽

...

Keyword(s):

Gene Family ◽

Leaf Senescence ◽

Leucine Zipper ◽

Class Iii

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Faculty Opinions recommendation of CORONA, a member of the class III homeodomain leucine zipper gene family in Arabidopsis, regulates stem cell specification and organogenesis.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1022753.287748 ◽

2005 ◽

Author(s):

Mark Running

Keyword(s):

Stem Cell ◽

Gene Family ◽

Leucine Zipper ◽

Class Iii ◽

Cell Specification

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CORONA, a Member of the Class III Homeodomain Leucine Zipper Gene Family in Arabidopsis, Regulates Stem Cell Specification and Organogenesis

The Plant Cell ◽

10.1105/tpc.104.026179 ◽

2005 ◽

Vol 17 (3) ◽

pp. 691-704 ◽

Cited By ~ 97

Author(s):

Kirsten A. Green ◽

Michael J. Prigge ◽

Rebecca B. Katzman ◽

Steven E. Clark

Keyword(s):

Stem Cell ◽

Gene Family ◽

Leucine Zipper ◽

Class Iii ◽

Cell Specification

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Roles of the 14-3-3 gene family in cotton flowering

BMC Plant Biology ◽

10.1186/s12870-021-02923-9 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Na Sang ◽

Hui Liu ◽

Bin Ma ◽

Xianzhong Huang ◽

Lu Zhuo ◽

...

Keyword(s):

Gene Family ◽

Protein Interactions ◽

Leucine Zipper ◽

Expression Patterns ◽

Bimolecular Fluorescence Complementation ◽

Structural Motif ◽

Virus Induced Gene Silencing ◽

Protein Protein Interactions ◽

Basic Leucine Zipper ◽

Genome Wide

Abstract Background In plants, 14-3-3 proteins, also called GENERAL REGULATORY FACTORs (GRFs), encoded by a large multigene family, are involved in protein–protein interactions and play crucial roles in various physiological processes. No genome-wide analysis of the GRF gene family has been performed in cotton, and their functions in flowering are largely unknown. Results In this study, 17, 17, 31, and 17 GRF genes were identified in Gossypium herbaceum, G. arboreum, G. hirsutum, and G. raimondii, respectively, by genome-wide analyses and were designated as GheGRFs, GaGRFs, GhGRFs, and GrGRFs, respectively. A phylogenetic analysis revealed that these proteins were divided into ε and non-ε groups. Gene structural, motif composition, synteny, and duplicated gene analyses of the identified GRF genes provided insights into the evolution of this family in cotton. GhGRF genes exhibited diverse expression patterns in different tissues. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that the GhGRFs interacted with the cotton FLOWERING LOCUS T homologue GhFT in the cytoplasm and nucleus, while they interacted with the basic leucine zipper transcription factor GhFD only in the nucleus. Virus-induced gene silencing in G. hirsutum and transgenic studies in Arabidopsis demonstrated that GhGRF3/6/9/15 repressed flowering and that GhGRF14 promoted flowering. Conclusions Here, 82 GRF genes were identified in cotton, and their gene and protein features, classification, evolution, and expression patterns were comprehensively and systematically investigated. The GhGRF3/6/9/15 interacted with GhFT and GhFD to form florigen activation complexs that inhibited flowering. However, GhGRF14 interacted with GhFT and GhFD to form florigen activation complex that promoted flowering. The results provide a foundation for further studies on the regulatory mechanisms of flowering.

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Insight into the bZIP Gene Family in Solanum tuberosum: Genome and Transcriptome Analysis to Understand the Roles of Gene Diversification in Spatiotemporal Gene Expression and Function

International Journal of Molecular Sciences ◽

10.3390/ijms22010253 ◽

2020 ◽

Vol 22 (1) ◽

pp. 253

Author(s):

Venura Herath ◽

Jeanmarie Verchot

Keyword(s):

Gene Expression ◽

Gene Family ◽

Functional Groups ◽

Leucine Zipper ◽

Expression Profiles ◽

Crop Improvement ◽

Potato Virus X ◽

Tissue Growth ◽

Abiotic Stress Response ◽

Sequence Alignments

The basic region-leucine zipper (bZIP) transcription factors (TFs) form homodimers and heterodimers via the coil–coil region. The bZIP dimerization network influences gene expression across plant development and in response to a range of environmental stresses. The recent release of the most comprehensive potato reference genome was used to identify 80 StbZIP genes and to characterize their gene structure, phylogenetic relationships, and gene expression profiles. The StbZIP genes have undergone 22 segmental and one tandem duplication events. Ka/Ks analysis suggested that most duplications experienced purifying selection. Amino acid sequence alignments and phylogenetic comparisons made with the Arabidopsis bZIP family were used to assign the StbZIP genes to functional groups based on the Arabidopsis orthologs. The patterns of introns and exons were conserved within the assigned functional groups which are supportive of the phylogeny and evidence of a common progenitor. Inspection of the leucine repeat heptads within the bZIP domains identified a pattern of attractive pairs favoring homodimerization, and repulsive pairs favoring heterodimerization. These patterns of attractive and repulsive heptads were similar within each functional group for Arabidopsis and S. tuberosum orthologs. High-throughput RNA-seq data indicated the most highly expressed and repressed genes that might play significant roles in tissue growth and development, abiotic stress response, and response to pathogens including Potato virus X. These data provide useful information for further functional analysis of the StbZIP gene family and their potential applications in crop improvement.

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Isolation and Characterization of Rat Cytochrome P-450IIB Gene Family Members

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)83538-4 ◽

1989 ◽

Vol 264 (12) ◽

pp. 7046-7053 ◽

Cited By ~ 3

Author(s):

C M Giachelli ◽

J Lin-Jones ◽

C J Omiecinski

Keyword(s):

Gene Family ◽

Family Members ◽

Isolation And Characterization

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Characterisation of the class III peroxidase gene family in carrot taproots and its role in anthocyanin and lignin accumulation

Plant Physiology and Biochemistry ◽

10.1016/j.plaphy.2021.08.004 ◽

2021 ◽

Author(s):

Geng Meng ◽

Weiyao Fan ◽

Søren K. Rasmussen

Keyword(s):

Gene Family ◽

Class Iii ◽

Peroxidase Gene ◽

Lignin Accumulation ◽

Class Iii Peroxidase

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Cloning and functional analysis of the FAD2 gene family from desert shrub Artemisia sphaerocephala

BMC Plant Biology ◽

10.1186/s12870-019-2083-5 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 2

Author(s):

Xiumei Miao ◽

Lijing Zhang ◽

Xiaowei Hu ◽

Shuzhen Nan ◽

Xiaolong Chen ◽

...

Keyword(s):

Fatty Acid ◽

Linoleic Acid ◽

Gene Family ◽

Fatty Acid Biosynthesis ◽

Family Members ◽

Pcr Analysis ◽

Mrna Levels ◽

Acid Biosynthesis ◽

Desert Shrub ◽

Artemisia Sphaerocephala

Abstract Background Linoleic acid is an important polyunsaturated fatty acid, required for all eukaryotes. Microsomal delta-12 (Δ12) oleate desaturase (FAD2) is a key enzyme for linoleic acid biosynthesis. Desert shrub Artemisia sphaerocephala is rich in linoleic acid, it has a large FAD2 gene family with twenty-six members. The aim of this work is to unveil the difference and potentially functionality of AsFAD2 family members. Results Full-length cDNAs of twenty-one AsFAD2 genes were obtained from A. sphaerocephala. The putative polypeptides encoded by AsFAD2 family genes showed a high level of sequence similarity and were relatively conserved during evolution. The motif composition was also relatively conservative. Quantitative real-time PCR analysis revealed that the AsFAD2–1 gene was strongly expressed in developing seeds, which may be closely associated with the high accumulating ability of linoleic acid in A. sphaerocephala seeds. Although different AsFAD2 family members showed diverse response to salt stress, the overall mRNA levels of the AsFAD2 family genes was stable. Transient expression of AsFAD2 genes in the Nicotiana benthamiana leaves revealed that the encoded proteins were all located in the endoplasmic reticulum. Heterologous expression in Saccharomyces cerevisiae suggested that only three AsFAD2 enzymes, AsFAD2–1, − 10, and − 23, were Δ12 oleate desaturases, which could convert oleic acid to linoleic acid, whereas AsFAD2–1 and AsFAD2–10 could also produce palmitolinoleic acid. Conclusions This research reported the cloning, expression studies, subcellular localization and functional identification of the large AsFAD2 gene family. These results should be helpful in understanding fatty acid biosynthesis in A. sphaerocephala, and has the potential to be applied in the study of plant fatty acids traits.

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